Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Abstract:

:Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.

authors

Jones MB,Highlander SK,Anderson EL,Li W,Dayrit M,Klitgord N,Fabani MM,Seguritan V,Green J,Pride DT,Yooseph S,Biggs W,Nelson KE,Venter JC

doi

10.1073/pnas.1519288112

subject

Has Abstract

pub_date

2015-11-10 00:00:00

pages

14024-9

issue

45

eissn

0027-8424

issn

1091-6490

pii

1519288112

journal_volume

112

pub_type

杂志文章
  • An estrogen-dependent four-gene micronet regulating social recognition: a study with oxytocin and estrogen receptor-alpha and -beta knockout mice.

    abstract::Estrogens control many physiological and behavioral processes, some of which are connected to reproduction. These include sexual and other social behaviors. Here we implicate four gene products in a micronet required for mammalian social recognition, through which an individual learns to recognize other individuals. F...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0631699100

    authors: Choleris E,Gustafsson JA,Korach KS,Muglia LJ,Pfaff DW,Ogawa S

    更新日期:2003-05-13 00:00:00

  • Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors.

    abstract::PIF3 is a phytochrome-interacting basic helix-loop-helix transcription factor that negatively regulates light responses, including hypocotyl elongation, cotyledon opening, and hypocotyl negative gravitropism. However, the role of PIF3 in chlorophyll biosynthesis has not been clearly defined. Here, we show that PIF3 al...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0812219106

    authors: Shin J,Kim K,Kang H,Zulfugarov IS,Bae G,Lee CH,Lee D,Choi G

    更新日期:2009-05-05 00:00:00

  • A van der Waals-type equation of state for fluids with associating molecules.

    abstract::The basic assumptions of van der Waals theory are contained in two well-known concepts: excluded volume (repulsive forces) and a homogeneous, isotropic field potential (attractive forces). We have superimposed on these, one more well-known concept: the existence of dimers, trimers, etc., at chemical equilibrium. With ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.6.1773

    authors: Heidemann RA,Prausnitz JM

    更新日期:1976-06-01 00:00:00

  • Induction of a reductive pathway for deoxyribonucleotide synthesis during early embryogenesis of the sea urchin.

    abstract::Cell-free extracts of Arbacia eggs (Arbacia punctulata) apparently do not contain an enzymatic system for the reduction of ribonucleotides to deoxyribonucleotides. However, during an interval of 5 hr after fertilization at 23 degrees , an enzymatic system is produced that is capable of catalyzing the reduction of CDP ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.69.8.2006

    authors: Noronha JM,Sheys GH,Buchanan JM

    更新日期:1972-08-01 00:00:00

  • Conformational flexibility at the substrate binding site in the lactose permease of Escherichia coli.

    abstract::Glu-126 (helix IV) and Arg-144 (helix V) are charge paired and play a critical role in substrate binding in the lactose permease of Escherichia coli. When Glu-126 is replaced with Asp, the permease has relatively high activity, implying that helix V has sufficient flexibility to allow Arg-144 to accommodate the decrea...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.20.11178

    authors: Weinglass AB,Kaback HR

    更新日期:1999-09-28 00:00:00

  • Abrupt tropical climate change: past and present.

    abstract::Three lines of evidence for abrupt tropical climate change, both past and present, are presented. First, annually and decadally averaged delta(18)O and net mass-balance histories for the last 400 and 2,000 yr, respectively, demonstrate that the current warming at high elevations in the mid- to low latitudes is unprece...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0603900103

    authors: Thompson LG,Mosley-Thompson E,Brecher H,Davis M,León B,Les D,Lin PN,Mashiotta T,Mountain K

    更新日期:2006-07-11 00:00:00

  • Inhibition of the activation of Hageman factor (factor XII) by human vascular endothelial cell culture supernates.

    abstract::The supernatant fluid (conditioned medium) of cultured human vascular endothelial cells inhibits activation of Hageman factor (factor XII), whether by ellagic acid, bovine brain sulfatides, or bismuth subgallate; inhibition appears to be a property of one or more proteins in the culture supernates. This phenomenon may...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.23.10740

    authors: Ratnoff OD,Everson B,Embury P,Ziats NP,Anderson JM,Emanuelson MM,Malemud CJ

    更新日期:1991-12-01 00:00:00

  • Long-term perspective on wildfires in the western USA.

    abstract::Understanding the causes and consequences of wildfires in forests of the western United States requires integrated information about fire, climate changes, and human activity on multiple temporal scales. We use sedimentary charcoal accumulation rates to construct long-term variations in fire during the past 3,000 y in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.1112839109

    authors: Marlon JR,Bartlein PJ,Gavin DG,Long CJ,Anderson RS,Briles CE,Brown KJ,Colombaroli D,Hallett DJ,Power MJ,Scharf EA,Walsh MK

    更新日期:2012-02-28 00:00:00

  • Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs.

    abstract::The Escherichia coli mutS gene product is involved in mismatch correction in this organism. We have purified a biologically active form of the 97,000 Mr protein to near homogeneity from an overproducing strain. Enzymatic and chemical protection ("footprinting") experiments have demonstrated that mutS-encoded protein s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.14.5057

    authors: Su SS,Modrich P

    更新日期:1986-07-01 00:00:00

  • Dynamics of a protein matrix revealed by fluorescence quenching.

    abstract::The fluorescence of the supposedly buried tryptophan in ribonuclease T1 has been found to be collisionally quenched by acrylamide with a rate constant of 3 X 10(8) M--1 sec--1. Only a slight decrease in the quenching rate is observed upon a 5-fold increase in the viscosity of the solution. For this to be the case, the...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.72.9.3290

    authors: Eftink MR,Ghiron CA

    更新日期:1975-09-01 00:00:00

  • Optically functional isoxanthopterin crystals in the mirrored eyes of decapod crustaceans.

    abstract::The eyes of some aquatic animals form images through reflective optics. Shrimp, lobsters, crayfish, and prawns possess reflecting superposition compound eyes, composed of thousands of square-faceted eye units (ommatidia). Mirrors in the upper part of the eye (the distal mirror) reflect light collected from many ommati...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1722531115

    authors: Palmer BA,Hirsch A,Brumfeld V,Aflalo ED,Pinkas I,Sagi A,Rosenne S,Oron D,Leiserowitz L,Kronik L,Weiner S,Addadi L

    更新日期:2018-03-06 00:00:00

  • The HOX11 gene encodes a DNA-binding nuclear transcription factor belonging to a distinct family of homeobox genes.

    abstract::A translocation involving human chromosome 10, band q24, in a subset of T-cell acute leukemias disrupts a region surrounding the putative oncogene HOX11, which encodes a protein with a homeodomain. The HOX11 protein binds to a specific DNA sequence, it localizes to the cell nucleus, and it transactivates transcription...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.10.4431

    authors: Dear TN,Sanchez-Garcia I,Rabbitts TH

    更新日期:1993-05-15 00:00:00

  • Molecular flexibility can influence the stimulatory ability of receptor-ligand interactions at cell-cell junctions.

    abstract::Direct cell-cell communication is crucial for many processes in biology, particularly embryogenesis, interactions between hematopoetic cells, and in the nervous system. This communication is often mediated by the binding of receptors to cognate ligands at a cell-cell junction. One such interaction that is very importa...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0510991103

    authors: Qi S,Krogsgaard M,Davis MM,Chakraborty AK

    更新日期:2006-03-21 00:00:00

  • Immunoglobulins D and M mediate signals that are qualitatively different in B cells with an immature phenotype.

    abstract::The CH family of murine B-cell lymphomas includes several members that are sensitive to growth inhibition when their membrane IgM (mIgM) receptors are cross-linked by anti-mu chain, anti-kappa chain, or anti-idiotypic antibodies. These lymphomas are IgM+, Ia+, and IgD +/- and resemble neonatal B cells in terms of thei...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.18.6919

    authors: Alés-Martínez JE,Warner GL,Scott DW

    更新日期:1988-09-01 00:00:00

  • Complete cloning and sequencing of rat gp330/"megalin," a distinctive member of the low density lipoprotein receptor gene family.

    abstract::We completed the cDNA cloning and sequencing of gp330, the major kidney glomerular antigen for rat Heymann nephritis. The deduced 4660-aa sequence, expected to constitute a mature protein of M(r) 516,715, consists of a probable N-terminal signal peptide sequence (25 aa), an extracellular region (4400 aa), a single tra...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.21.9725

    authors: Saito A,Pietromonaco S,Loo AK,Farquhar MG

    更新日期:1994-10-11 00:00:00

  • Viruses in fungi: infection of yeast with the K1 and K2 killer viruses.

    abstract::We demonstrate here that yeast killer viruses, previously thought to be transmitted only by cytoplasmic mixing during division, mating, or other induced forms of cell fusion, are capable of extracellular transmission. Viral particles from standard K1 and K2 killer strains were used to inoculate sensitive cells of Sacc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.12.4293

    authors: el-Sherbeini M,Bostian KA

    更新日期:1987-06-01 00:00:00

  • Brief history of US debt limits before 1939.

    abstract::Between 1776 and 1920, the US Congress designed more than 200 distinct securities and stated the maximum amount of each that the Treasury could sell. Between 1917 and 1939, Congress gradually delegated all decisions about designing US debt instruments to the Treasury. In 1939, Congress began imposing a limit on the pa...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1719687115

    authors: Hall GJ,Sargent TJ

    更新日期:2018-03-20 00:00:00

  • Strong triaxial coupling and anomalous Poisson effect in collagen networks.

    abstract::While cells within tissues generate and sense 3D states of strain, the current understanding of the mechanics of fibrous extracellular matrices (ECMs) stems mainly from uniaxial, biaxial, and shear tests. Here, we demonstrate that the multiaxial deformations of fiber networks in 3D cannot be inferred solely based on t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1815659116

    authors: Ban E,Wang H,Franklin JM,Liphardt JT,Janmey PA,Shenoy VB

    更新日期:2019-04-02 00:00:00

  • An NAD+-dependent transcriptional program governs self-renewal and radiation resistance in glioblastoma.

    abstract::Accumulating evidence suggests cancer cells exhibit a dependency on metabolic pathways regulated by nicotinamide adenine dinucleotide (NAD+). Nevertheless, how the regulation of this metabolic cofactor interfaces with signal transduction networks remains poorly understood in glioblastoma. Here, we report nicotinamide ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1610921114

    authors: Gujar AD,Le S,Mao DD,Dadey DY,Turski A,Sasaki Y,Aum D,Luo J,Dahiya S,Yuan L,Rich KM,Milbrandt J,Hallahan DE,Yano H,Tran DD,Kim AH

    更新日期:2016-12-20 00:00:00

  • Nonconscious activation of placebo and nocebo pain responses.

    abstract::The dominant theories of human placebo effects rely on a notion that consciously perceptible cues, such as verbal information or distinct stimuli in classical conditioning, provide signals that activate placebo effects. However, growing evidence suggest that behavior can be triggered by stimuli presented outside of co...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,随机对照试验

    doi:10.1073/pnas.1202056109

    authors: Jensen KB,Kaptchuk TJ,Kirsch I,Raicek J,Lindstrom KM,Berna C,Gollub RL,Ingvar M,Kong J

    更新日期:2012-09-25 00:00:00

  • Thyroid hormone modulates glucose production via a sympathetic pathway from the hypothalamic paraventricular nucleus to the liver.

    abstract::Thyrotoxicosis increases endogenous glucose production (EGP) and induces hepatic insulin resistance. We have recently shown that these alterations can be modulated by selective hepatic sympathetic and parasympathetic denervation, pointing to neurally mediated effects of thyroid hormone on glucose metabolism. Here, we ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0805355106

    authors: Klieverik LP,Janssen SF,van Riel A,Foppen E,Bisschop PH,Serlie MJ,Boelen A,Ackermans MT,Sauerwein HP,Fliers E,Kalsbeek A

    更新日期:2009-04-07 00:00:00

  • Optimal functionalization of a molecular electrocatalyst for hydride transfer.

    abstract::Optimization of hydride transfer (HT) catalysts to enhance rates and selectivities of (photo)electroreduction reactions could be a crucial component of a sustainable chemical industry. Here, we analyze how ring functionalization of the adsorbed transient intermediate 2-pyridinide (2-PyH-*)-predicted to form in situ fr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1911948116

    authors: Xu S,Carter EA

    更新日期:2019-11-12 00:00:00

  • Equatorial convergence of India and early Cenozoic climate trends.

    abstract::India's northward flight and collision with Asia was a major driver of global tectonics in the Cenozoic and, we argue, of atmospheric CO(2) concentration (pCO(2)) and thus global climate. Subduction of Tethyan oceanic crust with a carpet of carbonate-rich pelagic sediments deposited during transit beneath the high-pro...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.0805382105

    authors: Kent DV,Muttoni G

    更新日期:2008-10-21 00:00:00

  • Iron-carbon bond lengths in carbonmonoxy and cyanomet complexes of the monomeric hemoglobin III from Chironomus thummi thummi: a critical comparison between resonance Raman and x-ray diffraction studies.

    abstract::Soret-excited resonance Raman spectroscopy yields direct information regarding the iron-carbon bonding interactions in the cyanomet and carbonmonoxy complexes of hemoglobin III from Chironomus thummi thummi (CTT III) in solution. By isotope exchange in cyanide (13CN-, C15N-, and 13C15N-) and carbon monoxide (13CO, C18...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.16.5106

    authors: Yu NT,Benko B,Kerr EA,Gersonde K

    更新日期:1984-08-01 00:00:00

  • Isolation of a high-affinity stable single-chain Fv specific for mesothelin from DNA-immunized mice by phage display and construction of a recombinant immunotoxin with anti-tumor activity.

    abstract::Mesothelin is a differentiation antigen present on the surface of ovarian cancers, mesotheliomas, and several other types of human cancers. Because among normal tissues, mesothelin is present only on mesothelial cells, it represents a good target for antibody-mediated delivery of cytotoxic agents. In the present study...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.2.669

    authors: Chowdhury PS,Viner JL,Beers R,Pastan I

    更新日期:1998-01-20 00:00:00

  • Stigmergy, collective actions, and animal social spacing.

    abstract::Collective animal behavior studies have led the way in developing models that account for a large number of individuals, but mostly have considered situations in which alignment and attraction play a key role, such as in schooling and flocking. By quantifying how animals react to one another's presence, when interacti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1307071110

    authors: Giuggioli L,Potts JR,Rubenstein DI,Levin SA

    更新日期:2013-10-15 00:00:00

  • White lines in L-edge x-ray absorption spectra and their implications for anomalous diffraction studies of biological materials.

    abstract::We have measured high-resolution x-ray absorption spectra of lanthanide (Ln) and heavy transition metal complexes that display prominent narrow absorption peaks near the L2 and L3 absorption edges. The anomalous scattering factors (f' and f"), which are mathematically related to the absorption cross section, have corr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.10.5884

    authors: Lye RC,Phillips JC,Kaplan D,Doniach S,Hodgson KO

    更新日期:1980-10-01 00:00:00

  • Calcium-myristoyl protein switch.

    abstract::Recoverin, a recently discovered member of the EF-hand superfamily of Ca(2+)-binding proteins, serves as a Ca2+ sensor in vision. The amino terminus of the protein from retinal rod cells contains a covalently attached myristoyl or related N-acyl group. We report here studies of unmyristoylated and myristoylated recomb...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.23.11569

    authors: Zozulya S,Stryer L

    更新日期:1992-12-01 00:00:00

  • Enigma, a mitochondrial protein affecting lifespan and oxidative stress response in Drosophila.

    abstract::Deregulation of energy metabolism by external interventions or mutations in metabolic genes can extend lifespan in a wide range of species. We describe mutations in Drosophila melanogaster that confer resistance to oxidative stress and display a longevity phenotype. These phenotypes are associated with molecular lesio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0510564103

    authors: Mourikis P,Hurlbut GD,Artavanis-Tsakonas S

    更新日期:2006-01-31 00:00:00

  • Functional identification of the hematopoietic stem cell niche in the ventral domain of the embryonic dorsal aorta.

    abstract::The first definitive/adult-type hematopoietic stem cells (HSCs) in the mouse aorta-gonad-mesonephros region emerge between embryonic days 10.5 and 11.5. The discovery of clusters of hematopoietic cells on the ventral luminal surface of the dorsal aorta in various vertebrate species has led to speculation that the floo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0700984104

    authors: Taoudi S,Medvinsky A

    更新日期:2007-05-29 00:00:00