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Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.

Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF.

Genome Res. 2013 Jan;23(1):111-20. doi: 10.1101/gr.142315.112. Epub 2012 Aug 30.


Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life.

Xiong W, Brown CT, Morowitz MJ, Banfield JF, Hettich RL.

Microbiome. 2017 Jul 10;5(1):72. doi: 10.1186/s40168-017-0290-6.


Strain-resolved community genomic analysis of gut microbial colonization in a premature infant.

Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF.

Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1128-33. doi: 10.1073/pnas.1010992108. Epub 2010 Dec 29. Erratum in: Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4512.


A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.

Wang M, Ye Y, Tang H.

J Comput Biol. 2012 Jun;19(6):814-25. doi: 10.1089/cmb.2012.0058.


Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant.

Brooks B, Mueller RS, Young JC, Morowitz MJ, Hettich RL, Banfield JF.

Front Microbiol. 2015 Jul 1;6:654. doi: 10.3389/fmicb.2015.00654. eCollection 2015.


The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing.

Drell T, Lutsar I, Stšepetova J, Parm U, Metsvaht T, Ilmoja ML, Simm J, Sepp E.

Gut Microbes. 2014 May-Jun;5(3):304-12. doi: 10.4161/gmic.28849.


Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations.

Willner D, Low S, Steen JA, George N, Nimmo GR, Schembri MA, Hugenholtz P.

MBio. 2014 Feb 25;5(2):e01064-13. doi: 10.1128/mBio.01064-13.


Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.

Martínez-del Campo A, Bodea S, Hamer HA, Marks JA, Haiser HJ, Turnbaugh PJ, Balskus EP.

MBio. 2015 Apr 14;6(2). pii: e00042-15. doi: 10.1128/mBio.00042-15.


Temporal dynamics of the very premature infant gut dominant microbiota.

Aujoulat F, Roudière L, Picaud JC, Jacquot A, Filleron A, Neveu D, Baum TP, Marchandin H, Jumas-Bilak E.

BMC Microbiol. 2014 Dec 31;14:325. doi: 10.1186/s12866-014-0325-0.


Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development.

Raveh-Sadka T, Thomas BC, Singh A, Firek B, Brooks B, Castelle CJ, Sharon I, Baker R, Good M, Morowitz MJ, Banfield JF.

Elife. 2015 Mar 3;4. doi: 10.7554/eLife.05477.


Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case.

Young JC, Pan C, Adams RM, Brooks B, Banfield JF, Morowitz MJ, Hettich RL.

Proteomics. 2015 Oct;15(20):3463-73. doi: 10.1002/pmic.201400563. Epub 2015 Jul 21.


Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data.

Jeraldo P, Hernandez A, Nielsen HB, Chen X, White BA, Goldenfeld N, Nelson H, Alhquist D, Boardman L, Chia N.

Front Microbiol. 2016 May 26;7:783. doi: 10.3389/fmicb.2016.00783. eCollection 2016.


Comparison between terminal-restriction fragment length polymorphism (T-RFLP) and quantitative culture for analysis of infants' gut microbiota.

Sjöberg F, Nowrouzian F, Rangel I, Hannoun C, Moore E, Adlerberth I, Wold AE.

J Microbiol Methods. 2013 Jul;94(1):37-46. doi: 10.1016/j.mimet.2013.04.002. Epub 2013 Apr 11.


Farnesoid X Receptor Signaling Shapes the Gut Microbiota and Controls Hepatic Lipid Metabolism.

Zhang L, Xie C, Nichols RG, Chan SH, Jiang C, Hao R, Smith PB, Cai J, Simons MN, Hatzakis E, Maranas CD, Gonzalez FJ, Patterson AD.

mSystems. 2016 Oct 11;1(5). pii: e00070-16. eCollection 2016 Sep-Oct.


Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs.

Hu P, Tom L, Singh A, Thomas BC, Baker BJ, Piceno YM, Andersen GL, Banfield JF.

MBio. 2016 Jan 19;7(1):e01669-15. doi: 10.1128/mBio.01669-15.


Intestinal microflora in early infancy: composition and development.

Fanaro S, Chierici R, Guerrini P, Vigi V.

Acta Paediatr Suppl. 2003 Sep;91(441):48-55.


Microbiome assembly across multiple body sites in low-birthweight infants.

Costello EK, Carlisle EM, Bik EM, Morowitz MJ, Relman DA.

MBio. 2013 Oct 29;4(6):e00782-13. doi: 10.1128/mBio.00782-13.


Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants.

Raveh-Sadka T, Firek B, Sharon I, Baker R, Brown CT, Thomas BC, Morowitz MJ, Banfield JF.

ISME J. 2016 Dec;10(12):2817-2830. doi: 10.1038/ismej.2016.83. Epub 2016 Jun 3.


Assembly-driven community genomics of a hypersaline microbial ecosystem.

Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE.

PLoS One. 2013 Apr 18;8(4):e61692. doi: 10.1371/journal.pone.0061692. Print 2013.

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