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Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders.

Díaz-Sánchez S, Perrotta AR, Rockafellow I, Alm EJ, Okimoto R, Hawken R, Hanning I.

PLoS One. 2019 May 7;14(5):e0216080. doi: 10.1371/journal.pone.0216080. eCollection 2019.


Adaptive Evolution within Gut Microbiomes of Healthy People.

Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ.

Cell Host Microbe. 2019 May 8;25(5):656-667.e8. doi: 10.1016/j.chom.2019.03.007. Epub 2019 Apr 23.


Transmission of human-associated microbiota along family and social networks.

Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ.

Nat Microbiol. 2019 Mar 25. doi: 10.1038/s41564-019-0409-6. [Epub ahead of print]


Interactions in self-assembled microbial communities saturate with diversity.

Yu X, Polz MF, Alm EJ.

ISME J. 2019 Jun;13(6):1602-1617. doi: 10.1038/s41396-019-0356-5. Epub 2019 Feb 26.


Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut.

Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ.

Science. 2019 Jan 11;363(6423):181-187. doi: 10.1126/science.aau5238.


Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK.

Sci Transl Med. 2018 Dec 19;10(472). pii: eaap8914. doi: 10.1126/scitranslmed.aap8914.


Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.

Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.

Gut Microbes. 2018 Oct 29:1-9. doi: 10.1080/19490976.2018.1528822. [Epub ahead of print]


Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort.

Gurry T; HST Microbiome Consortium*, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ.

Sci Rep. 2018 Aug 23;8(1):12699. doi: 10.1038/s41598-018-30783-1.


Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal.

Kearney SM, Gibbons SM, Erdman SE, Alm EJ.

Cell Rep. 2018 Aug 14;24(7):1842-1851. doi: 10.1016/j.celrep.2018.07.032.


Metagenomic mining of regulatory elements enables programmable species-selective gene expression.

Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH.

Nat Methods. 2018 May;15(5):323-329. doi: 10.1038/nmeth.4633. Epub 2018 Mar 19.


Defining the gut microbiota in individuals with periodontal diseases: an exploratory study.

Lourenςo TGB, Spencer SJ, Alm EJ, Colombo APV.

J Oral Microbiol. 2018 Jul 3;10(1):1487741. doi: 10.1080/20002297.2018.1487741. eCollection 2018.


Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota.

Kearney SM, Gibbons SM, Poyet M, Gurry T, Bullock K, Allegretti JR, Clish CB, Alm EJ.

ISME J. 2018 Oct;12(10):2403-2416. doi: 10.1038/s41396-018-0192-z. Epub 2018 Jun 13.


Searching for superstool: maximizing the therapeutic potential of FMT.

Olesen SW, Leier MM, Alm EJ, Kahn SA.

Nat Rev Gastroenterol Hepatol. 2018 Jul;15(7):387-388. doi: 10.1038/s41575-018-0019-4. No abstract available.


Correcting for batch effects in case-control microbiome studies.

Gibbons SM, Duvallet C, Alm EJ.

PLoS Comput Biol. 2018 Apr 23;14(4):e1006102. doi: 10.1371/journal.pcbi.1006102. eCollection 2018 Apr.


Random sequences rapidly evolve into de novo promoters.

Yona AH, Alm EJ, Gore J.

Nat Commun. 2018 Apr 18;9(1):1530. doi: 10.1038/s41467-018-04026-w.


Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates.

Corzett CH, Elsherbini J, Chien DM, Hehemann JH, Henschel A, Preheim SP, Yu X, Alm EJ, Polz MF.

J Bacteriol. 2018 Jul 10;200(15). pii: e00020-18. doi: 10.1128/JB.00020-18. Print 2018 Aug 1.


Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.


Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ.

Cell Host Microbe. 2018 Feb 14;23(2):229-240.e5. doi: 10.1016/j.chom.2018.01.003.


High resolution time series reveals cohesive but short-lived communities in coastal plankton.

Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, Polz MF.

Nat Commun. 2018 Jan 18;9(1):266. doi: 10.1038/s41467-017-02571-4.


Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.

Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ.

Nat Commun. 2017 Dec 5;8(1):1784. doi: 10.1038/s41467-017-01973-8.


Salt-responsive gut commensal modulates TH17 axis and disease.

Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN.

Nature. 2017 Nov 30;551(7682):585-589. doi: 10.1038/nature24628. Epub 2017 Nov 15.


Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment.

Pakpour S, Bhanvadia A, Zhu R, Amarnani A, Gibbons SM, Gurry T, Alm EJ, Martello LA.

Microbiome. 2017 Nov 13;5(1):148. doi: 10.1186/s40168-017-0368-1.


dbOTU3: A new implementation of distribution-based OTU calling.

Olesen SW, Duvallet C, Alm EJ.

PLoS One. 2017 May 4;12(5):e0176335. doi: 10.1371/journal.pone.0176335. eCollection 2017.


Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2017 Apr 6;544(7648):124. doi: 10.1038/nature20774. Epub 2017 Mar 22. No abstract available.


Unraveling the processes shaping mammalian gut microbiomes over evolutionary time.

Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ.

Nat Commun. 2017 Feb 23;8:14319. doi: 10.1038/ncomms14319.


Two dynamic regimes in the human gut microbiome.

Gibbons SM, Kearney SM, Smillie CS, Alm EJ.

PLoS Comput Biol. 2017 Feb 21;13(2):e1005364. doi: 10.1371/journal.pcbi.1005364. eCollection 2017 Feb.


Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor.

Perrotta AR, Kumaraswamy R, Bastidas-Oyanedel JR, Alm EJ, Rodríguez J.

PLoS One. 2017 Feb 14;12(2):e0171369. doi: 10.1371/journal.pone.0171369. eCollection 2017.


Designing fecal microbiota transplant trials that account for differences in donor stool efficacy.

Olesen SW, Gurry T, Alm EJ.

Stat Methods Med Res. 2018 Oct;27(10):2906-2917. doi: 10.1177/0962280216688502. Epub 2017 Feb 9.


A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio.

Chu ND, Clarke SA, Timberlake S, Polz MF, Grossman AD, Alm EJ.

MBio. 2017 Feb 7;8(1). pii: e02045-16. doi: 10.1128/mBio.02045-16.


Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations.

Chu ND, Smith MB, Perrotta AR, Kassam Z, Alm EJ.

PLoS One. 2017 Jan 26;12(1):e0170922. doi: 10.1371/journal.pone.0170922. eCollection 2017.


Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

King AJ, Preheim SP, Bailey KL, Robeson MS 2nd, Roy Chowdhury T, Crable BR, Hurt RA Jr, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin AP, Elias DA.

Environ Sci Technol. 2017 Mar 7;51(5):2879-2889. doi: 10.1021/acs.est.6b04751. Epub 2017 Feb 10.


Dysbiosis is not an answer.

Olesen SW, Alm EJ.

Nat Microbiol. 2016 Nov 25;1:16228. doi: 10.1038/nmicrobiol.2016.228. No abstract available.


Microbial lysate upregulates host oxytocin.

Varian BJ, Poutahidis T, DiBenedictis BT, Levkovich T, Ibrahim Y, Didyk E, Shikhman L, Cheung HK, Hardas A, Ricciardi CE, Kolandaivelu K, Veenema AH, Alm EJ, Erdman SE.

Brain Behav Immun. 2017 Mar;61:36-49. doi: 10.1016/j.bbi.2016.11.002. Epub 2016 Nov 5.


Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes.

Hehemann JH, Arevalo P, Datta MS, Yu X, Corzett CH, Henschel A, Preheim SP, Timberlake S, Alm EJ, Polz MF.

Nat Commun. 2016 Sep 22;7:12860. doi: 10.1038/ncomms12860.


Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem.

Preheim SP, Olesen SW, Spencer SJ, Materna A, Varadharajan C, Blackburn M, Friedman J, Rodríguez J, Hemond H, Alm EJ.

Nat Microbiol. 2016 Aug 15;1(9):16130. doi: 10.1038/nmicrobiol.2016.130.


Virtual microfluidics for digital quantification and single-cell sequencing.

Xu L, Brito IL, Alm EJ, Blainey PC.

Nat Methods. 2016 Sep;13(9):759-62. doi: 10.1038/nmeth.3955. Epub 2016 Aug 1.


Mobile genes in the human microbiome are structured from global to individual scales.

Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ.

Nature. 2016 Jul 21;535(7612):435-439. doi: 10.1038/nature18927. Epub 2016 Jul 13. Erratum in: Nature. 2017 Apr 6;544(7648):124.


Erratum to: Host lifestyle affects human microbiota on daily timescales.

David LA, Materna AC, Friedman J, Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ.

Genome Biol. 2016 May 31;17(1):117. No abstract available.


Tracking Strains in the Microbiome: Insights from Metagenomics and Models.

Brito IL, Alm EJ.

Front Microbiol. 2016 May 19;7:712. doi: 10.3389/fmicb.2016.00712. eCollection 2016. Review.


A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, Hazen TC, Alm EJ.

PLoS One. 2016 May 6;11(5):e0154804. doi: 10.1371/journal.pone.0154804. eCollection 2016.


Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R.

ISME J. 2016 Jul;10(7):1669-81. doi: 10.1038/ismej.2015.235. Epub 2016 Feb 23.


Clostridium difficile associated risk of death score (CARDS): a novel severity score to predict mortality among hospitalised patients with C. difficile infection.

Kassam Z, Cribb Fabersunne C, Smith MB, Alm EJ, Kaplan GG, Nguyen GC, Ananthakrishnan AN.

Aliment Pharmacol Ther. 2016 Mar;43(6):725-33. doi: 10.1111/apt.13546. Epub 2016 Feb 5.


Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Juhani Virta MP, Alm EJ.

ISME J. 2016 Feb;10(2):427-36. doi: 10.1038/ismej.2015.124. Epub 2015 Sep 22.


Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.

Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ.

Nat Biotechnol. 2015 Oct;33(10):1053-60. doi: 10.1038/nbt.3329. Epub 2015 Sep 14.


Natural bacterial communities serve as quantitative geochemical biosensors.

Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC.

MBio. 2015 May 12;6(3):e00326-15. doi: 10.1128/mBio.00326-15.


Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code.

Fournier GP, Alm EJ.

J Mol Evol. 2015 Apr;80(3-4):171-85. doi: 10.1007/s00239-015-9672-1. Epub 2015 Mar 20.


'Hygienic' lymphocytes convey increased cancer risk.

Levkovich T, Poutahidis T, Cappelle K, Smith MB, Perrotta A, Alm EJ, Erdman SE.

J Anal Oncol. 2014 Aug 12;3(3):113-121.


Dietary microbes modulate transgenerational cancer risk.

Poutahidis T, Varian BJ, Levkovich T, Lakritz JR, Mirabal S, Kwok C, Ibrahim YM, Kearney SM, Chatzigiagkos A, Alm EJ, Erdman SE.

Cancer Res. 2015 Apr 1;75(7):1197-204. doi: 10.1158/0008-5472.CAN-14-2732. Epub 2015 Feb 25.


Improved gene tree error correction in the presence of horizontal gene transfer.

Bansal MS, Wu YC, Alm EJ, Kellis M.

Bioinformatics. 2015 Apr 15;31(8):1211-8. doi: 10.1093/bioinformatics/btu806. Epub 2014 Dec 5.


Transfer of noncoding DNA drives regulatory rewiring in bacteria.

Oren Y, Smith MB, Johns NI, Kaplan Zeevi M, Biran D, Ron EZ, Corander J, Wang HH, Alm EJ, Pupko T.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16112-7. doi: 10.1073/pnas.1413272111. Epub 2014 Oct 13.

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