Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.

Abstract:

:To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled the de novo reconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. Two Halomonas spp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequence coverage (9× to 2,700×) within the metagenomic data set.

journal_name

Appl Environ Microbiol

authors

Nelson WC,Maezato Y,Wu YW,Romine MF,Lindemann SR

doi

10.1128/AEM.02274-15

subject

Has Abstract

pub_date

2015-10-23 00:00:00

pages

255-67

issue

1

eissn

0099-2240

issn

1098-5336

pii

AEM.02274-15

journal_volume

82

pub_type

杂志文章
  • Sequence variability of P2-like prophage genomes carrying the cytolethal distending toxin V operon in Escherichia coli O157.

    abstract::Cytolethal distending toxins (CDT) are potent cytotoxins of several Gram-negative pathogenic bacteria, including Escherichia coli, in which five types (CDT-I to CDT-V) have been identified so far. CDT-V is frequently associated with Shiga-toxigenic E. coli (STEC), enterohemorrhagic E. coli (EHEC) O157 strains, and str...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01134-13

    authors: Sváb D,Horváth B,Maróti G,Dobrindt U,Tóth I

    更新日期:2013-08-01 00:00:00

  • Chronic Airway Colonization by Achromobacter xylosoxidans in Cystic Fibrosis Patients Is Not Sustained by Their Domestic Environment.

    abstract::Achromobacter spp. are nonfermentative Gram-negative bacilli considered emergent pathogens in cystic fibrosis (CF). Although some cross-transmission events between CF patients have been described, Achromobacter strains were mostly patient specific, suggesting sporadic acquisitions from nonhuman reservoirs. However, so...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01739-18

    authors: Dupont C,Jumas-Bilak E,Doisy C,Aujoulat F,Chiron R,Marchandin H

    更新日期:2018-11-15 00:00:00

  • Modeling of pathogen survival during simulated gastric digestion.

    abstract::The objective of the present study was to develop a mathematical model of pathogenic bacterial inactivation kinetics in a gastric environment in order to further understand a part of the infectious dose-response mechanism. The major bacterial pathogens Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella s...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.02139-10

    authors: Koseki S,Mizuno Y,Sotome I

    更新日期:2011-02-01 00:00:00

  • Isolation of Azospirillum lipoferum 4T Tn5 Mutants Affected in Melanization and Laccase Activity.

    abstract::Azospirillum lipoferum 4T has original properties such as nonmotility, melanin synthesis, and laccase activity. Following random Tn5 mutagenesis in A. lipoferum 4T, we obtained 10 mutants which were affected in melanization and laccase activity. The class 1 mutants, with intermediate levels of laccase activity, showed...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.60.9.3413-3415.1994

    authors: Faure D,Bouillant ML,Bally R

    更新日期:1994-09-01 00:00:00

  • In vivo and in vitro binding of Vip3Aa to Spodoptera frugiperda midgut and characterization of binding sites by (125)I radiolabeling.

    abstract::Bacillus thuringiensis vegetative insecticidal proteins (Vip3A) have been recently introduced in important crops as a strategy to delay the emerging resistance to the existing Cry toxins. The mode of action of Vip3A proteins has been studied in Spodoptera frugiperda with the aim of characterizing their binding to the ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01521-14

    authors: Chakroun M,Ferré J

    更新日期:2014-10-01 00:00:00

  • Absence of microbial mineralization of lignin in anaerobic enrichment cultures.

    abstract::The existence of anaerobic biodegradation of lignin was examined in mixed microflora. Egyptian soil samples, in which rapid mineralization of organic matter takes place in the presence of an important anaerobic microflora, were used to obtain the anaerobic enrichment cultures for this study. Specifically, 14CO2 or [14...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.46.3.661-665.1983

    authors: Odier E,Monties B

    更新日期:1983-09-01 00:00:00

  • Inactivation of adenoviruses, enteroviruses, and murine norovirus in water by free chlorine and monochloramine.

    abstract::Inactivation of infectious viruses during drinking water treatment is usually achieved with free chlorine. Many drinking water utilities in the United States now use monochloramine as a secondary disinfectant to minimize disinfectant by-product formation and biofilm growth. The inactivation of human adenoviruses 2, 40...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01342-09

    authors: Cromeans TL,Kahler AM,Hill VR

    更新日期:2010-02-01 00:00:00

  • Viruses as partners in spring bloom microbial trophodynamics.

    abstract::Population sizes of algae, bacteria, heterotrophic flagellates, and viruses were observed through the 1989 spring diatom bloom in Raunefjorden in western Norway. The culmination of the diatom bloom was followed by a peak in the concentration of bacteria and an increase in the concentration of heterotrophic flagellates...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.56.5.1400-1405.1990

    authors: Bratbak G,Heldal M,Norland S,Thingstad TF

    更新日期:1990-05-01 00:00:00

  • Estimation of bacterial nitrate reduction rates at in situ concentrations in freshwater sediments.

    abstract::A method was developed to follow bacterial nitrate reduction in freshwater sediments by using common high-performance liquid chromatographic equipment. The low detection limit (14 pmol) of the method enabled us to study concentration profiles and reaction kinetics under natural conditions. Significant nitrate concentr...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.53.2.217-223.1987

    authors: Hordijk CA,Snieder M,van Engelen JJ,Cappenberg TE

    更新日期:1987-02-01 00:00:00

  • Inhibition of plant-pathogenic bacteria by short synthetic cecropin A-melittin hybrid peptides.

    abstract::Short peptides of 11 residues were synthesized and tested against the economically important plant pathogenic bacteria Erwinia amylovora, Pseudomonas syringae, and Xanthomonas vesicatoria and compared to the previously described peptide Pep3 (WKLFKKILKVL-NH(2)). The antimicrobial activity of Pep3 and 22 analogues was ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.72.5.3302-3308.2006

    authors: Ferre R,Badosa E,Feliu L,Planas M,Montesinos E,Bardají E

    更新日期:2006-05-01 00:00:00

  • Cross-institute evaluations of inhibitor-resistant PCR reagents for direct testing of aerosol and blood samples containing biological warfare agent DNA.

    abstract::Rapid pathogen detection is crucial for the timely introduction of therapeutics. Two groups (one in the United Kingdom and one in the United States) independently evaluated inhibitor-resistant PCR reagents for the direct testing of substrates. In the United Kingdom, a multiplexed Bacillus anthracis (target) and Bacill...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.03478-13

    authors: Minogue TD,Rachwal PA,Trombley Hall A,Koehler JW,Weller SA

    更新日期:2014-02-01 00:00:00

  • Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI).

    abstract::Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U....

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/aem.69.12.7467-7479.2003

    authors: Petrie L,North NN,Dollhopf SL,Balkwill DL,Kostka JE

    更新日期:2003-12-01 00:00:00

  • Expression of a Clostridium thermocellum endoglucanase gene in Lactobacillus plantarum.

    abstract::Recombinant plasmid pM25 containing the celE gene of Clostridium thermocellum, which codes for an enzymatically active endoglucanase, was transformed into Lactobacillus plantarum by electroporation. Strains harboring pM25 expressed thermostable endoglucanase, which was found predominantly in the culture medium. Two ot...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.55.8.2095-2097.1989

    authors: Bates EE,Gilbert HJ,Hazlewood GP,Huckle J,Laurie JI,Mann SP

    更新日期:1989-08-01 00:00:00

  • Unique substrate spectrum and PCR application of Nanoarchaeum equitans family B DNA polymerase.

    abstract::The known archaeal family B DNA polymerases are unable to participate in the PCR in the presence of uracil. Here, we report on a novel archaeal family B DNA polymerase from Nanoarchaeum equitans that can successfully utilize deaminated bases such as uracil and hypoxanthine and on its application to PCR. N. equitans fa...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00624-08

    authors: Choi JJ,Song JG,Nam KH,Lee JI,Bae H,Kim GA,Sun Y,Kwon ST

    更新日期:2008-11-01 00:00:00

  • Responses of Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus to simulated food processing treatments, determined using fluorescence-activated cell sorting and plate counting.

    abstract::Three common food pathogenic microorganisms were exposed to treatments simulating those used in food processing. Treated cell suspensions were then analyzed for reduction in growth by plate counting. Flow cytometry (FCM) and fluorescence-activated cell sorting (FACS) were carried out on treated cells stained for membr...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00323-11

    authors: Kennedy D,Cronin UP,Wilkinson MG

    更新日期:2011-07-01 00:00:00

  • Use of an Escherichia coli recombinant producing thermostable polyphosphate kinase as an ATP regenerator to produce fructose 1,6-diphosphate.

    abstract::Heat-treated Escherichia coli producing Thermus polyphosphate kinase regenerated ATP by using exogenous polyphosphate. This recombinant could be used as a platform to produce valuable compounds in combination with thermostable phosphorylating or energy-requiring enzymes. In this work, we demonstrated the production of...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00278-07

    authors: Iwamoto S,Motomura K,Shinoda Y,Urata M,Kato J,Takiguchi N,Ohtake H,Hirota R,Kuroda A

    更新日期:2007-09-01 00:00:00

  • Regio-selective 10-hydroxylation of patchoulol, a sesquiterpene, by pithomyces species.

    abstract::Of some 350 microorganisms screened, four strains of Pithomyces species were found to carry out regio-selective hydroxylation of patchoulol, a sesquiterpene, to 10-hydroxypatchoulol: Pithomyces sp. NRJ201, P. chartarum NRJ210, and, to a lesser extent, P. cynodontis ATCC 26150 and P. atro-olivaceus IFO 6651 were found ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.42.2.187-191.1981

    authors: Suhara Y,Itoh S,Ogawa M,Yokose K,Sawada T,Sano T,Ninomiya R,Maruyama HB

    更新日期:1981-08-01 00:00:00

  • Pathogenicity of Listeria monocytogenes grown on crabmeat.

    abstract::The pathogenicity of Listeria monocytogenes as influenced by growth on crabmeat at 5 and 10 degrees C was studied. Crabmeat was inoculated with L. monocytogenes V7 (ca. 10(4) CFU/g) and incubated for up to 14 days at 5 and 10 degrees C. At selected incubation times, L. monocytogenes was removed from crabmeat by washin...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.56.5.1216-1220.1990

    authors: Brackett RE,Beuchat LR

    更新日期:1990-05-01 00:00:00

  • Comparative Analysis of Extremely Thermophilic Caldicellulosiruptor Species Reveals Common and Unique Cellular Strategies for Plant Biomass Utilization.

    abstract::Microbiological, genomic and transcriptomic analyses were used to examine three species from the bacterial genus Caldicellulosiruptor with respect to their capacity to convert the carbohydrate content of lignocellulosic biomass at 70°C to simple sugars, acetate, lactate, CO2, and H2. Caldicellulosiruptor bescii, C. kr...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01622-15

    authors: Zurawski JV,Conway JM,Lee LL,Simpson HJ,Izquierdo JA,Blumer-Schuette S,Nookaew I,Adams MW,Kelly RM

    更新日期:2015-10-01 00:00:00

  • Bacterial fermentation of cheese whey for production of a ruminant feed supplement rich in curde protein.

    abstract::A simple and efficient process for the production of a ruminant feed supplement, rich in crude protein (defined as total N X 6.25), by bacterial fermentation of cheese whey has been developed. The lactose in unpasteurized whey is fermented to lactate acid by Lactobacillus bulgaricus at a temperature of 43 degrees C an...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.32.6.769-776.1976

    authors: Reddy CA,Henderson HE,Erdman MD

    更新日期:1976-12-01 00:00:00

  • Expression of a novel small antimicrobial protein from the seeds of motherwort (Leonurus japonicus) confers disease resistance in tobacco.

    abstract::Medicinal plants are valuable resources of natural antimicrobial materials. A novel small protein with antimicrobial activities, designated LJAMP1, was purified from the seeds of a medicinal herb, motherwort (Leonurus japonicus Houtt). LJAMP1 is a heat-stable protein with a molecular mass of 7.8 kDa and a determined i...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.02016-06

    authors: Yang X,Xiao Y,Wang X,Pei Y

    更新日期:2007-02-01 00:00:00

  • Anaerobic utilization of phosphite and hypophosphite by Bacillus sp.

    abstract::A Bacillus sp. capable of utilizing phosphite and hypophosphite under anaerobic conditions was isolated from Cape Canerval soil samples. The organism was isolated on a glucose-mineral salts medium with phosphate deleted. Anaerobic cultivation of this isolate resulted in decreases in the hypophosphite or phosphite conc...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.35.5.937-944.1978

    authors: Foster TL,Winans L Jr,Helms SJ

    更新日期:1978-05-01 00:00:00

  • Reductive dehalogenation and conversion of 2-chlorophenol to 3-chlorobenzoate in a methanogenic sediment community: implications for predicting the environmental fate of chlorinated pollutants.

    abstract::Biotransformation of 2-chlorophenol by a methanogenic sediment community resulted in the transient accumulation of phenol and benzoate. 3-Chlorobenzoate was a more persistent product of 2-chlorophenol metabolism. The anaerobic biotransformation of phenol to benzoate presumably occurred via para-carboxylation and dehyd...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.65.11.5169-5172.1999

    authors: Becker JG,Stahl DA,Rittmann BE

    更新日期:1999-11-01 00:00:00

  • Novel Capsular Polysaccharide Loci and New Diagnostic Tools for High-Throughput Capsular Gene Typing in Streptococcus suis.

    abstract::Streptococcus suis is an important pathogen of pigs and may cause serious disease in humans. Serotyping is an important tool for detection and epidemiological studies of S. suis Thirty-three reference serotypes and nine novel cps loci (NCLs) are recognized in S. suis To gain a better understanding of the prevalence an...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.02102-16

    authors: Qiu X,Bai X,Lan R,Zheng H,Xu J

    更新日期:2016-11-21 00:00:00

  • Expression of the laccase gene from a white rot fungus in Pichia pastoris can enhance the resistance of this yeast to H2O2-mediated oxidative stress by stimulating the glutathione-based antioxidative system.

    abstract::Laccase is a copper-containing polyphenol oxidase that has great potential in industrial and biotechnological applications. Previous research has suggested that fungal laccase may be involved in the defense against oxidative stress, but there is little direct evidence supporting this hypothesis, and the mechanism by w...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.00218-12

    authors: Yang Y,Fan F,Zhuo R,Ma F,Gong Y,Wan X,Jiang M,Zhang X

    更新日期:2012-08-01 00:00:00

  • Single-Cell Protein Production by the Acid-Tolerant Fungus Scytalidium acidophilum from Acid Hydrolysates of Waste Paper.

    abstract::The bioconversion of waste paper to single-cell protein at pH <1 by Scytalidium acidophilum is described. Waste paper pretreated with 72% H(2)SO(4) at 4 degrees C was diluted with water to a pH of <0.1 and hydrolyzed. This yielded an adequate sugar-containing substrate for the growth of the fungus. A total of 97% of t...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.43.3.643-647.1982

    authors: Ivarson KC,Morita H

    更新日期:1982-03-01 00:00:00

  • Heat inactivation of Mycobacterium avium-Mycobacterium intracellulare complex organisms in meat products.

    abstract::Wieners and sausages were prepared which contained the most heat-tolerant representative of the Mycobacterium avium-Mycobacterium intracellulare complex we were able to obtain. They also were prepared with infected tissues obtained from tuberculous swine. Processing conditions were as varied as possible. Neither incor...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.38.5.831-835.1979

    authors: Merkal RS,Crawford JA,Whipple DL

    更新日期:1979-11-01 00:00:00

  • Common occurrence of plasmid DNA and vancomycin resistance in Leuconostoc spp.

    abstract::Resistance to vancomycin permitted detection, in a culture of Streptococcus cremoris 290PC, of a contaminant gram-positive coccus. Morphological and physiological characteristics indicated that this bacterium was a strain of Leuconostoc sp., designated PO184. This strain contained four plasmid species, which were dist...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.48.6.1129-1133.1984

    authors: Orberg PK,Sandine WE

    更新日期:1984-12-01 00:00:00

  • Algicidal Activity of Streptomyces eurocidicus JXJ-0089 Metabolites and Their Effects on Microcystis Physiology.

    abstract:UNLABELLED:Copper sulfate (CuSO4) has been widely used as an algicide to control harmful cyanobacterial blooms (CyanoHABs) in freshwater lakes. However, there are increasing concerns about this application, due mainly to the general toxicity of CuSO4 to other aquatic species and its long-term persistence in the environ...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.01198-16

    authors: Zhang BH,Ding ZG,Li HQ,Mou XZ,Zhang YQ,Yang JY,Zhou EM,Li WJ

    更新日期:2016-08-15 00:00:00

  • Fate of the biological control agent Pseudomonas aureofaciens TX-1 after application to turfgrass.

    abstract::The fate and impact of Pseudomonas aureofaciens TX-1 following application as a biocontrol agent for fungi in turfgrass were studied. The organism was applied with a modified irrigation system by using a preparation containing 1 x 10(6) P. aureofaciens TX-1 CFU ml(-1) about 100 times between May and August. We examine...

    journal_title:Applied and environmental microbiology

    pub_type: 杂志文章

    doi:10.1128/AEM.67.8.3542-3548.2001

    authors: Sigler WV,Nakatsu CH,Reicher ZJ,Turco RF

    更新日期:2001-08-01 00:00:00