Mathematical modeling of primary succession of murine intestinal microbiota

Proceedings of the National Academy of Sciences of the United States of America
Simeone MarinoPatrick D Schloss

Abstract

Understanding the nature of interpopulation interactions in host-associated microbial communities is critical to understanding gut colonization, responses to perturbations, and transitions between health and disease. Characterizing these interactions is complicated by the complexity of these communities and the observation that even if populations can be cultured, their in vitro and in vivo phenotypes differ significantly. Dynamic models are the cornerstone of computational systems biology and a key objective of computational systems biologists is the reconstruction of biological networks (i.e., network inference) from high-throughput data. When such computational models reflect biology, they provide an opportunity to generate testable hypotheses as well as to perform experiments that are impractical or not feasible in vivo or in vitro. We modeled time-series data for murine microbial communities using statistical approaches and systems of ordinary differential equations. To obtain the dense time-series data, we sequenced the 16S ribosomal RNA (rRNA) gene from DNA isolated from the fecal material of germfree mice colonized with cecal contents of conventionally raised animals. The modeling results suggested a lack of mutualistic...Continue Reading

References

Feb 1, 1983·Infection and Immunity·R FreterK E Carey
Sep 21, 1995·Journal of Theoretical Biology·D E Kirschner, M J Blaser
Dec 1, 2004·Annual Review of Genetics·Christian S RiesenfeldJo Handelsman
Sep 9, 2006·Journal of Bioinformatics and Computational Biology·Simeone Marino, Eberhard O Voit
Dec 22, 2006·Nature·Ruth E LeyJeffrey I Gordon
Jun 26, 2007·Applied and Environmental Microbiology·Qiong WangJames R Cole
Jun 28, 2007·PLoS Biology·Chana PalmerPatrick O Brown
Apr 2, 2009·Proceedings of the National Academy of Sciences of the United States of America·J P O'DwyerJ L Green
Apr 7, 2010·Science Translational Medicine·Peter J TurnbaughJeffrey I Gordon
Jun 23, 2010·Proceedings of the National Academy of Sciences of the United States of America·Maria G Dominguez-BelloRob Knight
Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jeremy E KoenigRuth E Ley
Feb 1, 2011·BMC Bioinformatics·Christopher QuincePeter J Turnbaugh
Mar 23, 2011·Applied and Environmental Microbiology·Patrick D Schloss, Sarah L Westcott
May 21, 2011·Science·Jeremiah J FaithJeffrey I Gordon
Jun 28, 2011·Bioinformatics·Robert C EdgarRob Knight
Aug 19, 2011·The ISME Journal·Jack A GilbertDawn Field
Sep 3, 2011·Science·Gary D WuJames D Lewis
Sep 9, 2011·The ISME Journal·Albert BarberánNoah Fierer
Jan 25, 2012·Archives of Internal Medicine·Zain KassamChristine H Lee
Jan 31, 2012·Applied and Environmental Microbiology·Merritt G GillillandGary B Huffnagle
Jun 13, 2012·Gut Microbes·Patrick D SchlossJoseph F Petrosino
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Jul 19, 2012·PLoS Computational Biology·Karoline FaustCurtis Huttenhower
Aug 10, 2012·PLoS Computational Biology·Georg K GerberLynn Bry
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Nov 28, 2012·PLoS Biology·Jonas Schluter, Kevin R Foster

❮ Previous
Next ❯

Citations

Aug 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Patricio S La RosaPhillip I Tarr
Apr 15, 2014·Journal of Molecular Biology·Vanni Bucci, Joao B Xavier
Jun 4, 2014·The ISME Journal·Peter De Schryver, Olav Vadstein
Mar 4, 2014·FEBS Letters·Georg K Gerber
Feb 9, 2016·Scientific Reports·Michael J McGeachieAugusto Litonjua
Jul 6, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Vanessa O Ezenwa, Allison E Williams
Dec 24, 2015·Environmental Microbiology·Ana LokmerKarl Mathias Wegner
Jun 20, 2014·Immunological Reviews·Marcus Fulde, Mathias W Hornef
Sep 5, 2015·BMC Systems Biology·Kun-Nan TsaiDaryi Wang
Aug 4, 2015·Journal of the Royal Society, Interface·Xiang-Yi LiArne Traulsen
Jan 13, 2015·Annual Review of Immunology·Silvia Caballero, Eric G Pamer
Jun 24, 2015·PLoS Computational Biology·Steven N SteinwayReka Albert
May 8, 2015·PLoS Computational Biology·Zachary D KurtzRichard A Bonneau
Sep 16, 2016·Frontiers in Microbiology·Ana LokmerK Mathias Wegner
Dec 22, 2016·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Hong-Tai CaoYang-Yu Liu
Feb 20, 2016·PloS One·Tatiana ShashkovaVadim Govorun
Feb 13, 2016·PLoS Computational Biology·Travis E GibsonYang-Yu Liu
Apr 25, 2018·Nature Reviews. Microbiology·Katerina V-A Johnson, Kevin R Foster
Oct 22, 2017·Applied and Environmental Microbiology·Richard KevorkianKaren G Lloyd
Jun 16, 2016·MSphere·Joseph P ZackularPatrick D Schloss
Mar 21, 2018·Genes & Nutrition·Bastian HornungPeter J Schaap
Aug 9, 2017·The ISME Journal·Benjamin J RidenhourChristopher H Remien
May 20, 2014·Current Opinion in Gastroenterology·Christos PolytarchouDimitrios Iliopoulos
Nov 2, 2019·Proceedings of the National Academy of Sciences of the United States of America·Burcu TepekuleSebastian Bonhoeffer
Jul 3, 2019·Infection and Immunity·Aman KumarVanessa Sperandio
May 30, 2020·PLoS Computational Biology·Tyler A JosephItsik Pe'er
Oct 4, 2019·Nature Reviews. Microbiology·Gino VranckenJeroen Raes
Apr 6, 2017·Frontiers in Microbiology·Akshay MalwadeBrian P Ingalls
Apr 1, 2017·BMC Genomics·Mustafa AlshawaqfehAhmad Bani Younes
Mar 19, 2019·Experimental Biology and Medicine·Anders B Dohlman, Xiling Shen
Oct 25, 2016·Microbes and Environments·Camilla KristoffersenKnut Rudi
Mar 24, 2016·NPJ Systems Biology and Applications·Phuongan DamEberhard O Voit
Nov 27, 2016·BMC Bioinformatics·Grace Tzun-Wen ShawDaryi Wang
Dec 28, 2017·PLoS Computational Biology·Chieh Lo, Radu Marculescu

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.