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Items: 1 to 50 of 182

1.

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research.

Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, Livny J, Vlamakis H, Clish C, Bullock K, Deik A, Scott J, Pierce KA, Xavier RJ, Alm EJ.

Nat Med. 2019 Sep;25(9):1442-1452. doi: 10.1038/s41591-019-0559-3. Epub 2019 Sep 2.

PMID:
31477907
2.

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
3.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.

Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

PMID:
31341288
4.

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors.

Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ.

BMC Immunol. 2019 Jun 21;20(1):19. doi: 10.1186/s12865-019-0300-5.

5.

A practical guide to methods controlling false discoveries in computational biology.

Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC.

Genome Biol. 2019 Jun 4;20(1):118. doi: 10.1186/s13059-019-1716-1.

6.

Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities.

Miller JI, Techtmann S, Fortney J, Mahmoudi N, Joyner D, Liu J, Olesen S, Alm E, Fernandez A, Gardinali P, GaraJayeva N, Askerov FS, Hazen TC.

Front Microbiol. 2019 May 9;10:995. doi: 10.3389/fmicb.2019.00995. eCollection 2019.

7.

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function.

Duvallet C, Larson K, Snapper S, Iosim S, Lee A, Freer K, May K, Alm E, Rosen R.

PLoS One. 2019 May 20;14(5):e0216453. doi: 10.1371/journal.pone.0216453. eCollection 2019.

8.

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.

9.

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.

PMID:
31028005
10.

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 Jun;4(6):964-971. doi: 10.1038/s41564-019-0409-6. Epub 2019 Mar 25.

PMID:
30911128
11.

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.

PMID:
30809013
12.

Comparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics.

Learman DR, Ahmad Z, Brookshier A, Henson MW, Hewitt V, Lis A, Morrison C, Robinson A, Todaro E, Wologo E, Wynne S, Alm EW, Kourtev PS.

PeerJ. 2019 Jan 14;6:e6258. doi: 10.7717/peerj.6258. eCollection 2019.

13.

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.

14.

The rise and fall of a vancomycin-resistant clone of Enterococcus faecium among broilers in Sweden.

Nilsson O, Alm E, Greko C, Bengtsson B.

J Glob Antimicrob Resist. 2019 Jun;17:233-235. doi: 10.1016/j.jgar.2018.12.013. Epub 2019 Jan 3.

PMID:
30611929
15.

(Un)safe spaces, affective labour and perceived health among people with trans experiences living in Sweden.

Linander I, Goicolea I, Alm E, Hammarström A, Harryson L.

Cult Health Sex. 2019 Aug;21(8):914-928. doi: 10.1080/13691058.2018.1527038. Epub 2019 Jan 2.

PMID:
30601097
16.

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.

PMID:
30567928
17.

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. 2019;10(3):358-366. doi: 10.1080/19490976.2018.1528822. Epub 2018 Oct 29.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

PMID:
29899513
23.

Detection of Influenza A viruses at migratory bird stopover sites in Michigan, USA.

Lickfett TM, Clark E, Gehring TM, Alm EW.

Infect Ecol Epidemiol. 2018 May 18;8(1):1474709. doi: 10.1080/20008686.2018.1474709. eCollection 2018.

24.

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.

PMID:
29703976
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

Potential for gulls to transport bacteria from human waste sites to beaches.

Alm EW, Daniels-Witt QR, Learman DR, Ryu H, Jordan DW, Gehring TM, Santo Domingo J.

Sci Total Environ. 2018 Feb 15;615:123-130. doi: 10.1016/j.scitotenv.2017.09.232. Epub 2017 Sep 28.

PMID:
28964987
35.

Improving the genotyping resolution of Cryptosporidium hominis subtype IbA10G2 using one step PCR-based amplicon sequencing.

Beser J, Hallström BM, Advani A, Andersson S, Östlund G, Winiecka-Krusnell J, Lebbad M, Alm E, Troell K, Arrighi RBG.

Infect Genet Evol. 2017 Nov;55:297-304. doi: 10.1016/j.meegid.2017.08.035. Epub 2017 Sep 23.

PMID:
28919550
36.

Reply.

Bajaj JS, Kassam Z, Cox IJ, Gurry T, Williams R, Alm E, John B, Smith M, Taylor-Robinson SD, Gillevet PM.

Hepatology. 2017 Oct;66(4):1355-1356. doi: 10.1002/hep.29368. Epub 2017 Aug 26. No abstract available.

37.

A nationwide outbreak of listeriosis associated with cold-cuts, Sweden 2013-2014.

Dahl V, Sundqvist L, Hedenström I, Löfdahl M, Alm E, Ringberg H, Lindblad M, Wallensten A, Thisted Lambertz S, Jernberg C.

Infect Ecol Epidemiol. 2017 Jun 13;7(1):1324232. doi: 10.1080/20008686.2017.1324232. eCollection 2017.

38.

Investigation of a food-borne outbreak of gastroenteritis in a school canteen revealed a variant of sapovirus genogroup V not detected by standard PCR, Sollentuna, Sweden, 2016.

Hergens MP, Nederby Öhd J, Alm E, Askling HH, Helgesson S, Insulander M, Lagerqvist N, Svenungsson B, Tihane M, Tolfvenstam T, Follin P.

Euro Surveill. 2017 Jun 1;22(22). pii: 30543. doi: 10.2807/1560-7917.ES.2017.22.22.30543.

39.

Fecal microbiota transplant from a rational stool donor improves hepatic encephalopathy: A randomized clinical trial.

Bajaj JS, Kassam Z, Fagan A, Gavis EA, Liu E, Cox IJ, Kheradman R, Heuman D, Wang J, Gurry T, Williams R, Sikaroodi M, Fuchs M, Alm E, John B, Thacker LR, Riva A, Smith M, Taylor-Robinson SD, Gillevet PM.

Hepatology. 2017 Dec;66(6):1727-1738. doi: 10.1002/hep.29306. Epub 2017 Oct 30.

40.

Emergence of vanA Enterococcus faecium in Denmark, 2005-15.

Hammerum AM, Baig S, Kamel Y, Roer L, Pinholt M, Gumpert H, Holzknecht B, Røder B, Justesen US, Samulioniené J, Kjærsgaard M, Østergaard C, Holm A, Dzajic E, Søndergaard TS, Gaini S, Edquist P, Alm E, Lilje B, Westh H, Stegger M, Hasman H.

J Antimicrob Chemother. 2017 Aug 1;72(8):2184-2190. doi: 10.1093/jac/dkx138.

PMID:
28541565
41.

"It was like I had to fit into a category": Care-seekers' experiences of gender regulation in the Swedish trans-specific healthcare.

Linander I, Alm E, Goicolea I, Harryson L.

Health (London). 2019 Jan;23(1):21-38. doi: 10.1177/1363459317708824. Epub 2017 May 19.

PMID:
28523938
42.

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.

43.

Non-pncA Gene-Mutated but Pyrazinamide-Resistant Mycobacterium tuberculosis: Why Is That?

Werngren J, Alm E, Mansjö M.

J Clin Microbiol. 2017 Jun;55(6):1920-1927. doi: 10.1128/JCM.02532-16. Epub 2017 Apr 12.

44.

A novel real-time PCR assay for specific detection of Brucella melitensis.

Kaden R, Ferrari S, Alm E, Wahab T.

BMC Infect Dis. 2017 Mar 24;17(1):230. doi: 10.1186/s12879-017-2327-7.

45.

Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments.

Park SH, Perrotta A, Hanning I, Diaz-Sanchez S, Pendleton S, Alm E, Ricke SC.

Poult Sci. 2017 Jun 1;96(6):1820-1830. doi: 10.3382/ps/pew441.

PMID:
28339946
46.

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.

PMID:
28329759
47.

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.

48.

Legionellosis acquired through a dental unit: a case study.

Schönning C, Jernberg C, Klingenberg D, Andersson S, Pääjärvi A, Alm E, Tano E, Lytsy B.

J Hosp Infect. 2017 May;96(1):89-92. doi: 10.1016/j.jhin.2017.01.009. Epub 2017 Jan 20.

PMID:
28228245
49.

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.

50.

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.

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