A distributed cell division counter reveals growth dynamics in the gut microbiota.

Abstract:

:Microbial population growth is typically measured when cells can be directly observed, or when death is rare. However, neither of these conditions hold for the mammalian gut microbiota, and, therefore, standard approaches cannot accurately measure the growth dynamics of this community. Here we introduce a new method (distributed cell division counting, DCDC) that uses the accurate segregation at cell division of genetically encoded fluorescent particles to measure microbial growth rates. Using DCDC, we can measure the growth rate of Escherichia coli for >10 consecutive generations. We demonstrate experimentally and theoretically that DCDC is robust to error across a wide range of temperatures and conditions, including in the mammalian gut. Furthermore, our experimental observations inform a mathematical model of the population dynamics of the gut microbiota. DCDC can enable the study of microbial growth during infection, gut dysbiosis, antibiotic therapy or other situations relevant to human health.

journal_name

Nat Commun

journal_title

Nature communications

authors

Myhrvold C,Kotula JW,Hicks WM,Conway NJ,Silver PA

doi

10.1038/ncomms10039

subject

Has Abstract

pub_date

2015-11-30 00:00:00

pages

10039

issn

2041-1723

pii

ncomms10039

journal_volume

6

pub_type

杂志文章
  • Intracellular interleukin-32γ mediates antiviral activity of cytokines against hepatitis B virus.

    abstract::Cytokines are involved in early host defense against pathogen infections. In particular, tumor necrosis factor (TNF) and interferon-gamma (IFN-γ) have critical functions in non-cytopathic elimination of hepatitis B virus (HBV) in hepatocytes. However, the molecular mechanisms and mediator molecules are largely unknown...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05782-5

    authors: Kim DH,Park ES,Lee AR,Park S,Park YK,Ahn SH,Kang HS,Won JH,Ha YN,Jae B,Kim DS,Chung WC,Song MJ,Kim KH,Park SH,Kim SH,Kim KH

    更新日期:2018-08-16 00:00:00

  • Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition.

    abstract::Helitrons are eukaryotic DNA transposons that have profoundly affected genome variability via capture and mobilization of host genomic sequences. Defining their mode of action is therefore important for understanding how genome landscapes evolve. Sequence similarities with certain prokaryotic mobile elements suggest a...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03688-w

    authors: Grabundzija I,Hickman AB,Dyda F

    更新日期:2018-03-29 00:00:00

  • ZEB1 turns into a transcriptional activator by interacting with YAP1 in aggressive cancer types.

    abstract::Early dissemination, metastasis and therapy resistance are central hallmarks of aggressive cancer types and the leading cause of cancer-associated deaths. The EMT-inducing transcriptional repressor ZEB1 is a crucial stimulator of these processes, particularly by coupling the activation of cellular motility with stemne...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10498

    authors: Lehmann W,Mossmann D,Kleemann J,Mock K,Meisinger C,Brummer T,Herr R,Brabletz S,Stemmler MP,Brabletz T

    更新日期:2016-02-15 00:00:00

  • Transient auditory nerve demyelination as a new mechanism for hidden hearing loss.

    abstract::Hidden hearing loss (HHL) is a recently described auditory neuropathy believed to contribute to speech discrimination and intelligibility deficits in people with normal audiological tests. Animals and humans with HHL have normal auditory thresholds but defective cochlear neurotransmission, that is, reduced suprathresh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms14487

    authors: Wan G,Corfas G

    更新日期:2017-02-17 00:00:00

  • A shape-shifting redox foldase contributes to Proteus mirabilis copper resistance.

    abstract::Copper resistance is a key virulence trait of the uropathogen Proteus mirabilis. Here we show that P. mirabilis ScsC (PmScsC) contributes to this defence mechanism by enabling swarming in the presence of copper. We also demonstrate that PmScsC is a thioredoxin-like disulfide isomerase but, unlike other characterized p...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms16065

    authors: Furlong EJ,Lo AW,Kurth F,Premkumar L,Totsika M,Achard MES,Halili MA,Heras B,Whitten AE,Choudhury HG,Schembri MA,Martin JL

    更新日期:2017-07-19 00:00:00

  • Nanosecond electron pulses in the analytical electron microscopy of a fast irreversible chemical reaction.

    abstract::We show how the kinetics of a fast and irreversible chemical reaction in a nanocrystalline material at high temperature can be studied using nanosecond electron pulses in an electron microscope. Infrared laser pulses first heat a nanocrystalline oxide layer on a carbon film, then single nanosecond electron pulses allo...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11669-w

    authors: Sinha SK,Khammari A,Picher M,Roulland F,Viart N,LaGrange T,Banhart F

    更新日期:2019-08-13 00:00:00

  • Shape-memory effects in molecular crystals.

    abstract::Molecular crystals can be bent elastically by expansion or plastically by delamination into slabs that glide along slip planes. Here we report that upon bending, terephthalic acid crystals can undergo a mechanically induced phase transition without delamination and their overall crystal integrity is retained. Such pla...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-11612-z

    authors: Ahmed E,Karothu DP,Warren M,Naumov P

    更新日期:2019-08-19 00:00:00

  • Integrating geological archives and climate models for the mid-Pliocene warm period.

    abstract::The mid-Pliocene Warm Period (mPWP) offers an opportunity to understand a warmer-than-present world and assess the predictive ability of numerical climate models. Environmental reconstruction and climate modelling are crucial for understanding the mPWP, and the synergy of these two, often disparate, fields has proven ...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/ncomms10646

    authors: Haywood AM,Dowsett HJ,Dolan AM

    更新日期:2016-02-16 00:00:00

  • Causality matters in medical imaging.

    abstract::Causal reasoning can shed new light on the major challenges in machine learning for medical imaging: scarcity of high-quality annotated data and mismatch between the development dataset and the target environment. A causal perspective on these issues allows decisions about data collection, annotation, preprocessing, a...

    journal_title:Nature communications

    pub_type: 杂志文章,评审

    doi:10.1038/s41467-020-17478-w

    authors: Castro DC,Walker I,Glocker B

    更新日期:2020-07-22 00:00:00

  • Structural basis of epilepsy-related ligand-receptor complex LGI1-ADAM22.

    abstract::Epilepsy is a common brain disorder throughout history. Epilepsy-related ligand-receptor complex, LGI1-ADAM22, regulates synaptic transmission and has emerged as a determinant of brain excitability, as their mutations and acquired LGI1 autoantibodies cause epileptic disorders in human. Here, we report the crystal stru...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03947-w

    authors: Yamagata A,Miyazaki Y,Yokoi N,Shigematsu H,Sato Y,Goto-Ito S,Maeda A,Goto T,Sanbo M,Hirabayashi M,Shirouzu M,Fukata Y,Fukata M,Fukai S

    更新日期:2018-04-18 00:00:00

  • Hierarchical nanostructured aluminum alloy with ultrahigh strength and large plasticity.

    abstract::High strength and high ductility are often mutually exclusive properties for structural metallic materials. This is particularly important for aluminum (Al)-based alloys which are widely commercially employed. Here, we introduce a hierarchical nanostructured Al alloy with a structure of Al nanograins surrounded by nan...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13087-4

    authors: Wu G,Liu C,Sun L,Wang Q,Sun B,Han B,Kai JJ,Luan J,Liu CT,Cao K,Lu Y,Cheng L,Lu J

    更新日期:2019-11-08 00:00:00

  • Control of electronic conduction at an oxide heterointerface using surface polar adsorbates.

    abstract::The interface between LaAlO(3) and SrTiO(3) possesses a range of intriguing properties, notably a proposed connection between the surface state of the LaAlO(3) and the conductivity buried in the SrTiO(3). Here we study the effect of the surface adsorption of a variety of common laboratory solvents on the conductivity ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms1501

    authors: Xie Y,Hikita Y,Bell C,Hwang HY

    更新日期:2011-10-11 00:00:00

  • Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA.

    abstract::Despite extensive studies on transcription mechanisms, it is unknown how termination complexes are disassembled, especially in what order the essential components dissociate. Our single-molecule fluorescence study unveils that RNA transcript release precedes RNA polymerase (RNAP) dissociation from the DNA template muc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-14200-3

    authors: Kang W,Ha KS,Uhm H,Park K,Lee JY,Hohng S,Kang C

    更新日期:2020-01-23 00:00:00

  • Tenomodulin promotes human adipocyte differentiation and beneficial visceral adipose tissue expansion.

    abstract::Proper regulation of energy storage in adipose tissue is crucial for maintaining insulin sensitivity and molecules contributing to this process have not been fully revealed. Here we show that type II transmembrane protein tenomodulin (TNMD) is upregulated in adipose tissue of insulin-resistant versus insulin-sensitive...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms10686

    authors: Senol-Cosar O,Flach RJ,DiStefano M,Chawla A,Nicoloro S,Straubhaar J,Hardy OT,Noh HL,Kim JK,Wabitsch M,Scherer PE,Czech MP

    更新日期:2016-02-16 00:00:00

  • Vimentin filaments interact with the actin cortex in mitosis allowing normal cell division.

    abstract::The vimentin network displays remarkable plasticity to support basic cellular functions and reorganizes during cell division. Here, we show that in several cell types vimentin filaments redistribute to the cell cortex during mitosis, forming a robust framework interwoven with cortical actin and affecting its organizat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12029-4

    authors: Duarte S,Viedma-Poyatos Á,Navarro-Carrasco E,Martínez AE,Pajares MA,Pérez-Sala D

    更新日期:2019-09-13 00:00:00

  • TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export.

    abstract::The metazoan TREX complex is recruited to mRNA during nuclear RNA processing and functions in exporting mRNA to the cytoplasm. Nxf1 is an mRNA export receptor, which binds processed mRNA and transports it through the nuclear pore complex. At present, the relationship between TREX and Nxf1 is not understood. Here we sh...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms2005

    authors: Viphakone N,Hautbergue GM,Walsh M,Chang CT,Holland A,Folco EG,Reed R,Wilson SA

    更新日期:2012-01-01 00:00:00

  • FRQ-CK1 interaction determines the period of circadian rhythms in Neurospora.

    abstract::Circadian clock mechanisms have been extensively investigated but the main rate-limiting step that determines circadian period remains unclear. Formation of a stable complex between clock proteins and CK1 is a conserved feature in eukaryotic circadian mechanisms. Here we show that the FRQ-CK1 interaction, but not FRQ ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-12239-w

    authors: Liu X,Chen A,Caicedo-Casso A,Cui G,Du M,He Q,Lim S,Kim HJ,Hong CI,Liu Y

    更新日期:2019-09-25 00:00:00

  • Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte.

    abstract::The survival of viruses partly relies on their ability to self-assemble inside host cells. Although coarse-grained simulations have identified different pathways leading to assembled virions from their components, experimental evidence is severely lacking. Here, we use time-resolved small-angle X-ray scattering to unc...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-05426-8

    authors: Chevreuil M,Law-Hine D,Chen J,Bressanelli S,Combet S,Constantin D,Degrouard J,Möller J,Zeghal M,Tresset G

    更新日期:2018-08-06 00:00:00

  • A general method for controlling and resolving rotational orientation of molecules in molecule-surface collisions.

    abstract::The outcome of molecule-surface collisions can be modified by pre-aligning the molecule; however, experiments accomplishing this are rare because of the difficulty of preparing molecules in aligned quantum states. Here we present a general solution to this problem based on magnetic manipulation of the rotational magne...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms15357

    authors: Godsi O,Corem G,Alkoby Y,Cantin JT,Krems RV,Somers MF,Meyer J,Kroes GJ,Maniv T,Alexandrowicz G

    更新日期:2017-05-08 00:00:00

  • Male-female communication triggers calcium signatures during fertilization in Arabidopsis.

    abstract::Cell-cell communication and interaction is critical during fertilization and triggers free cytosolic calcium ([Ca2+]cyto) as a key signal for egg activation and a polyspermy block in animal oocytes. Fertilization in flowering plants is more complex, involving interaction of a pollen tube with egg adjoining synergid ce...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms5645

    authors: Denninger P,Bleckmann A,Lausser A,Vogler F,Ott T,Ehrhardt DW,Frommer WB,Sprunck S,Dresselhaus T,Grossmann G

    更新日期:2014-08-22 00:00:00

  • A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays.

    abstract::A central problem in speciation is the origin and mechanisms of reproductive barriers that block gene flow between sympatric populations. Wind-pollinated plant species that flower in synchrony with one another rely on post-pollination interactions to maintain reproductive isolation. In some locations in Mexico, sympat...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-10259-0

    authors: Lu Y,Hokin SA,Kermicle JL,Hartwig T,Evans MMS

    更新日期:2019-05-24 00:00:00

  • Size-dependent kinetics during non-equilibrium lithiation of nano-sized zinc ferrite.

    abstract::Spinel transition metal oxides (TMOs) have emerged as promising anode materials for lithium-ion batteries. It has been shown that reducing their particle size to nanoscale dimensions benefits overall electrochemical performance. Here, we use in situ transmission electron microscopy to probe the lithiation behavior of ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-07831-5

    authors: Li J,Meng Q,Zhang Y,Peng L,Yu G,Marschilok AC,Wu L,Su D,Takeuchi KJ,Takeuchi ES,Zhu Y,Stach EA

    更新日期:2019-01-09 00:00:00

  • Control of chrysanthemum flowering through integration with an aging pathway.

    abstract::Age, as a threshold of floral competence acquisition, prevents precocious flowering when there is insufficient biomass, and ensures flowering independent of environmental conditions; however, the underlying regulatory mechanisms are largely unknown. In this study, silencing the expression of a nuclear factor gene, CmN...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00812-0

    authors: Wei Q,Ma C,Xu Y,Wang T,Chen Y,Lü J,Zhang L,Jiang CZ,Hong B,Gao J

    更新日期:2017-10-10 00:00:00

  • Imaging with a small number of photons.

    abstract::Low-light-level imaging techniques have application in many diverse fields, ranging from biological sciences to security. A high-quality digital camera based on a multi-megapixel array will typically record an image by collecting of order 10(5) photons per pixel, but by how much could this photon flux be reduced? In t...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/ncomms6913

    authors: Morris PA,Aspden RS,Bell JE,Boyd RW,Padgett MJ

    更新日期:2015-01-05 00:00:00

  • Marangoni-driven flower-like patterning of an evaporating drop spreading on a liquid substrate.

    abstract::Drop motility at liquid surfaces is attracting growing interest because of its potential applications in microfluidics and artificial cell design. Here we report the unique highly ordered pattern that sets in when a millimeter-size drop of dichloromethane spreads on an aqueous substrate under the influence of surface ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-018-03201-3

    authors: Wodlei F,Sebilleau J,Magnaudet J,Pimienta V

    更新日期:2018-02-26 00:00:00

  • Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability.

    abstract::Proteins are versatile natural building blocks with highly complex and multifunctional architectures, and self-assembled protein structures have been created by the introduction of covalent, noncovalent, or metal-coordination bonding. Here, we report the robust, selective, and reversible metal coordination properties ...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-13491-w

    authors: Yang M,Song WJ

    更新日期:2019-12-05 00:00:00

  • Author Correction: Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma.

    abstract::The original version of this Article contained an error in the spelling of a member of the PRACTICAL Consortium, Manuela Gago-Dominguez, which was incorrectly given as Manuela Gago Dominguez. This has now been corrected in both the PDF and HTML versions of the Article. Furthermore, in the original HTML version of this...

    journal_title:Nature communications

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41467-018-08107-8

    authors: Went M,Sud A,Försti A,Halvarsson BM,Weinhold N,Kimber S,van Duin M,Thorleifsson G,Holroyd A,Johnson DC,Li N,Orlando G,Law PJ,Ali M,Chen B,Mitchell JS,Gudbjartsson DF,Kuiper R,Stephens OW,Bertsch U,Broderick P,Ca

    更新日期:2019-01-10 00:00:00

  • Abnormal phase transition between two-dimensional high-density liquid crystal and low-density crystalline solid phases.

    abstract::Some two-dimensional liquid systems are theoretically predicted to have an anomalous phase transition due to unique intermolecular interactions, for example the first-order transition between two-dimensional high-density water and low-density amorphous ice. However, it has never been experimentally observed, to the be...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-02634-6

    authors: Li W,Kong L,Feng B,Fu H,Li H,Zeng XC,Wu K,Chen L

    更新日期:2018-01-15 00:00:00

  • White light emission from a single organic molecule with dual phosphorescence at room temperature.

    abstract::The development of single molecule white light emitters is extremely challenging for pure phosphorescent metal-free system at room temperature. Here we report a single pure organic phosphor, namely 4-chlorobenzoyldibenzothiophene, emitting white room temperature phosphorescence with Commission Internationale de l'Écla...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-017-00362-5

    authors: He Z,Zhao W,Lam JWY,Peng Q,Ma H,Liang G,Shuai Z,Tang BZ

    更新日期:2017-09-04 00:00:00

  • Two-dimensional molecular brush-functionalized porous bilayer composite separators toward ultrastable high-current density lithium metal anodes.

    abstract::Lithium metal batteries have been considerably limited by the problems of uncontrolled dendritic lithium formation and the highly reactive nature of lithium with electrolytes. Herein, we have developed functional porous bilayer composite separators by simply blade-coating polyacrylamide-grafted graphene oxide molecula...

    journal_title:Nature communications

    pub_type: 杂志文章

    doi:10.1038/s41467-019-09211-z

    authors: Li C,Liu S,Shi C,Liang G,Lu Z,Fu R,Wu D

    更新日期:2019-03-25 00:00:00