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Items: 1 to 50 of 210

1.

Microbiome profiling in extremely acidic soils affected by hydrothermal fluids: the case of the Solfatara Crater (Campi Flegrei, southern Italy).

Crognale S, Venturi S, Tassi F, Rossetti S, Rashed H, Cabassi J, Capecchiacci F, Nisi B, Vaselli O, Morrison HG, Sogin ML, Fazi S.

FEMS Microbiol Ecol. 2018 Dec 1;94(12). doi: 10.1093/femsec/fiy190.

PMID:
30247697
2.

Sex-specific associations of infants' gut microbiome with arsenic exposure in a US population.

Hoen AG, Madan JC, Li Z, Coker M, Lundgren SN, Morrison HG, Palys T, Jackson BP, Sogin ML, Cottingham KL, Karagas MR.

Sci Rep. 2018 Aug 22;8(1):12627. doi: 10.1038/s41598-018-30581-9.

3.

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.

Grahl N, Dolben EL, Filkins LM, Crocker AW, Willger SD, Morrison HG, Sogin ML, Ashare A, Gifford AH, Jacobs NJ, Schwartzman JD, Hogan DA.

mSphere. 2018 Aug 8;3(4). pii: e00292-18. doi: 10.1128/mSphere.00292-18.

4.

The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth.

Chernikova DA, Madan JC, Housman ML, Zain-Ul-Abideen M, Lundgren SN, Morrison HG, Sogin ML, Williams SM, Moore JH, Karagas MR, Hoen AG.

Pediatr Res. 2018 Jul;84(1):71-79. doi: 10.1038/s41390-018-0022-z. Epub 2018 May 23.

5.

Identification and Removal of Contaminant Sequences From Ribosomal Gene Databases: Lessons From the Census of Deep Life.

Sheik CS, Reese BK, Twing KI, Sylvan JB, Grim SL, Schrenk MO, Sogin ML, Colwell FS.

Front Microbiol. 2018 Apr 30;9:840. doi: 10.3389/fmicb.2018.00840. eCollection 2018.

6.

Seasonal Succession and Spatial Patterns of Synechococcus Microdiversity in a Salt Marsh Estuary Revealed through 16S rRNA Gene Oligotyping.

Mackey KRM, Hunter-Cevera K, Britten GL, Murphy LG, Sogin ML, Huber JA.

Front Microbiol. 2017 Aug 9;8:1496. doi: 10.3389/fmicb.2017.01496. eCollection 2017.

7.

The Microbiome and Human Biology.

Knight R, Callewaert C, Marotz C, Hyde ER, Debelius JW, McDonald D, Sogin ML.

Annu Rev Genomics Hum Genet. 2017 Aug 31;18:65-86. doi: 10.1146/annurev-genom-083115-022438. Epub 2017 Mar 20. Review.

PMID:
28375652
8.

Patient-Specific Bacteroides Genome Variants in Pouchitis.

Vineis JH, Ringus DL, Morrison HG, Delmont TO, Dalal S, Raffals LH, Antonopoulos DA, Rubin DT, Eren AM, Chang EB, Sogin ML.

MBio. 2016 Nov 15;7(6). pii: e01713-16. doi: 10.1128/mBio.01713-16.

9.

Editorial: New Insights into Microbial Ecology through Subtle Nucleotide Variation.

Eren AM, Sogin ML, Maignien L.

Front Microbiol. 2016 Aug 24;7:1318. doi: 10.3389/fmicb.2016.01318. eCollection 2016. No abstract available.

10.

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

Bálint M, Bahram M, Eren AM, Faust K, Fuhrman JA, Lindahl B, O'Hara RB, Öpik M, Sogin ML, Unterseher M, Tedersoo L.

FEMS Microbiol Rev. 2016 Sep;40(5):686-700. doi: 10.1093/femsre/fuw017. Epub 2016 Jun 29. Review.

PMID:
27358393
11.

Relationship of Bacterial Richness to Organic Degradation Rate and Sediment Age in Subseafloor Sediment.

Walsh EA, Kirkpatrick JB, Pockalny R, Sauvage J, Spivack AJ, Murray RW, Sogin ML, D'Hondt S.

Appl Environ Microbiol. 2016 Jul 29;82(16):4994-9. doi: 10.1128/AEM.00809-16. Print 2016 Aug 15.

12.

Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.

Ward MA, Pierre JF, Leal RF, Huang Y, Shogan B, Dalal SR, Weber CR, Leone VA, Musch MW, An GC, Rao MC, Rubin DT, Raffals LE, Antonopoulos DA, Sogin ML, Hyman NH, Alverdy JC, Chang EB.

Am J Physiol Gastrointest Liver Physiol. 2016 Jun 1;310(11):G973-88. doi: 10.1152/ajpgi.00017.2016. Epub 2016 Apr 14.

13.

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease.

Hogan DA, Willger SD, Dolben EL, Hampton TH, Stanton BA, Morrison HG, Sogin ML, Czum J, Ashare A.

PLoS One. 2016 Mar 4;11(3):e0149998. doi: 10.1371/journal.pone.0149998. eCollection 2016.

14.

Reply to Prince et al.: Ability of chemical dispersants to reduce oil spill impacts remains unclear.

Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML, Dittmar T, Passow U, Medeiros P, Joye SB.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1422-3. doi: 10.1073/pnas.1600498113. Epub 2016 Mar 1. No abstract available.

15.

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants.

Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HG, Sogin ML, Li H, Moore JH, Karagas MR.

JAMA Pediatr. 2016 Mar;170(3):212-9. doi: 10.1001/jamapediatrics.2015.3732.

16.

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves, Mammalia, and Actinopterygii.

Green HC, Fisher JC, McLellan SL, Sogin ML, Shanks OC.

Appl Environ Microbiol. 2015 Dec 28;82(5):1496-1503. doi: 10.1128/AEM.02456-15.

17.

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms.

Kleindienst S, Seidel M, Ziervogel K, Grim S, Loftis K, Harrison S, Malkin SY, Perkins MJ, Field J, Sogin ML, Dittmar T, Passow U, Medeiros PM, Joye SB.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14900-5. doi: 10.1073/pnas.1507380112. Epub 2015 Nov 9.

18.

Anvi'o: an advanced analysis and visualization platform for 'omics data.

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO.

PeerJ. 2015 Oct 8;3:e1319. doi: 10.7717/peerj.1319. eCollection 2015.

19.

Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.

Fisher JC, Eren AM, Green HC, Shanks OC, Morrison HG, Vineis JH, Sogin ML, McLellan SL.

Appl Environ Microbiol. 2015 Oct;81(20):7023-33. doi: 10.1128/AEM.01524-15. Epub 2015 Jul 31.

20.

Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.

Hoen AG, Li J, Moulton LA, O'Toole GA, Housman ML, Koestler DC, Guill MF, Moore JH, Hibberd PL, Morrison HG, Sogin ML, Karagas MR, Madan JC.

J Pediatr. 2015 Jul;167(1):138-47.e1-3. doi: 10.1016/j.jpeds.2015.02.049. Epub 2015 Mar 26.

21.

Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

Anderson RE, Sogin ML, Baross JA.

FEMS Microbiol Ecol. 2015 Jan;91(1):1-11. doi: 10.1093/femsec/fiu016. Epub 2014 Dec 5.

22.

Sewage reflects the microbiomes of human populations.

Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML.

MBio. 2015 Feb 24;6(2):e02574. doi: 10.1128/mBio.02574-14.

23.

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis.

Willger SD, Grim SL, Dolben EL, Shipunova A, Hampton TH, Morrison HG, Filkins LM, O'Toole GA, Moulton LA, Ashare A, Sogin ML, Hogan DA.

Microbiome. 2014 Nov 3;2:40. doi: 10.1186/2049-2618-2-40. eCollection 2014.

24.

Fetal exposures and perinatal influences on the stool microbiota of premature infants.

Chernikova DA, Koestler DC, Hoen AG, Housman ML, Hibberd PL, Moore JH, Morrison HG, Sogin ML, Zain-Ul-Abideen M, Madan JC.

J Matern Fetal Neonatal Med. 2016;29(1):99-105. doi: 10.3109/14767058.2014.987748. Epub 2015 Sep 4.

25.

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.

Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML.

ISME J. 2015 Mar 17;9(4):968-79. doi: 10.1038/ismej.2014.195.

26.

Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.

Anderson RE, Sogin ML, Baross JA.

PLoS One. 2014 Oct 3;9(10):e109696. doi: 10.1371/journal.pone.0109696. eCollection 2014.

27.

The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention.

Hampton TH, Green DM, Cutting GR, Morrison HG, Sogin ML, Gifford AH, Stanton BA, O'Toole GA.

Microbiome. 2014 Apr 28;2:14. doi: 10.1186/2049-2618-2-14. eCollection 2014.

28.

The microbiota regulates susceptibility to Fas-mediated acute hepatic injury.

Celaj S, Gleeson MW, Deng J, O'Toole GA, Hampton TH, Toft MF, Morrison HG, Sogin ML, Putra J, Suriawinata AA, Gorham JD.

Lab Invest. 2014 Sep;94(9):938-49. doi: 10.1038/labinvest.2014.93. Epub 2014 Jul 28.

29.

A single genus in the gut microbiome reflects host preference and specificity.

Eren AM, Sogin ML, Morrison HG, Vineis JH, Fisher JC, Newton RJ, McLellan SL.

ISME J. 2015 Jan;9(1):90-100. doi: 10.1038/ismej.2014.97. Epub 2014 Jun 17.

30.

Metagenomic analysis of the medicinal leech gut microbiota.

Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J.

Front Microbiol. 2014 Apr 17;5:151. doi: 10.3389/fmicb.2014.00151. eCollection 2014.

31.

Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.

Halliday E, McLellan SL, Amaral-Zettler LA, Sogin ML, Gast RJ.

PLoS One. 2014 Mar 5;9(3):e90815. doi: 10.1371/journal.pone.0090815. eCollection 2014.

32.

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.

Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE.

Microbiome. 2014 Feb 14;2(1):5. doi: 10.1186/2049-2618-2-5.

33.

VAMPS: a website for visualization and analysis of microbial population structures.

Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, Eren AM, Sogin ML.

BMC Bioinformatics. 2014 Feb 5;15:41. doi: 10.1186/1471-2105-15-41.

34.

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis.

Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML.

Microbiome. 2013 Mar 4;1(1):9. doi: 10.1186/2049-2618-1-9.

35.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM.

Microbiome. 2013 Mar 4;1(1):8. doi: 10.1186/2049-2618-1-8.

36.

Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation.

Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O'Toole GA.

Microbiome. 2013 Nov 1;1(1):27. doi: 10.1186/2049-2618-1-27.

37.

Host-specificity among abundant and rare taxa in the sponge microbiome.

Reveillaud J, Maignien L, Murat Eren A, Huber JA, Apprill A, Sogin ML, Vanreusel A.

ISME J. 2014 Jun;8(6):1198-209. doi: 10.1038/ismej.2013.227. Epub 2014 Jan 9.

38.

Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.

Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML.

Methods Ecol Evol. 2013 Dec 1;4(12). doi: 10.1111/2041-210X.12114.

39.

Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.

Gifford AH, Alexandru DM, Li Z, Dorman DB, Moulton LA, Price KE, Hampton TH, Sogin ML, Zuckerman JB, Parker HW, Stanton BA, O'Toole GA.

J Cyst Fibros. 2014 May;13(3):311-8. doi: 10.1016/j.jcf.2013.11.004. Epub 2013 Dec 13.

40.

Shifts in the microbial community composition of Gulf Coast beaches following beach oiling.

Newton RJ, Huse SM, Morrison HG, Peake CS, Sogin ML, McLellan SL.

PLoS One. 2013 Sep 10;8(9):e74265. doi: 10.1371/journal.pone.0074265. eCollection 2013. Erratum in: PLoS One. 2014;9(4):e94671.

41.

A filtering method to generate high quality short reads using illumina paired-end technology.

Eren AM, Vineis JH, Morrison HG, Sogin ML.

PLoS One. 2013 Jun 17;8(6):e66643. doi: 10.1371/journal.pone.0066643. Print 2013. Erratum in: PLoS One. 2013;8(6). doi:10.1371/annotation/afa5c40d-c604-46ae-84c4-82cb92193a5e.

42.

DRISEE overestimates errors in metagenomic sequencing data.

Eren AM, Morrison HG, Huse SM, Sogin ML.

Brief Bioinform. 2014 Sep;15(5):783-7. doi: 10.1093/bib/bbt010. Epub 2013 May 22.

43.

A microbial signature approach to identify fecal pollution in the waters off an urbanized coast of Lake Michigan.

Newton RJ, Bootsma MJ, Morrison HG, Sogin ML, McLellan SL.

Microb Ecol. 2013 May;65(4):1011-23. doi: 10.1007/s00248-013-0200-9. Epub 2013 Mar 9.

44.

Sewage reflects the distribution of human faecal Lachnospiraceae.

McLellan SL, Newton RJ, Vandewalle JL, Shanks OC, Huse SM, Eren AM, Sogin ML.

Environ Microbiol. 2013 Aug;15(8):2213-27. doi: 10.1111/1462-2920.12092. Epub 2013 Feb 25.

45.

Comparison of the microbial community structures of untreated wastewaters from different geographic locales.

Shanks OC, Newton RJ, Kelty CA, Huse SM, Sogin ML, McLellan SL.

Appl Environ Microbiol. 2013 May;79(9):2906-13. doi: 10.1128/AEM.03448-12. Epub 2013 Feb 22.

46.

Marine bacteria exhibit a bipolar distribution.

Sul WJ, Oliver TA, Ducklow HW, Amaral-Zettler LA, Sogin ML.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2342-7. doi: 10.1073/pnas.1212424110. Epub 2013 Jan 16.

47.

Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.

Madan JC, Koestler DC, Stanton BA, Davidson L, Moulton LA, Housman ML, Moore JH, Guill MF, Morrison HG, Sogin ML, Hampton TH, Karagas MR, Palumbo PE, Foster JA, Hibberd PL, O'Toole GA.

MBio. 2012 Aug 21;3(4). pii: e00251-12. doi: 10.1128/mBio.00251-12. Print 2012.

48.

Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability.

Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O'Toole GA.

J Bacteriol. 2012 Sep;194(17):4709-17. doi: 10.1128/JB.00566-12. Epub 2012 Jun 29.

49.

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.

Bowen JL, Morrison HG, Hobbie JE, Sogin ML.

ISME J. 2012 Nov;6(11):2014-23. doi: 10.1038/ismej.2012.47. Epub 2012 Jun 28.

50.

Gut microbial colonisation in premature neonates predicts neonatal sepsis.

Madan JC, Salari RC, Saxena D, Davidson L, O'Toole GA, Moore JH, Sogin ML, Foster JA, Edwards WH, Palumbo P, Hibberd PL.

Arch Dis Child Fetal Neonatal Ed. 2012 Nov;97(6):F456-62. doi: 10.1136/fetalneonatal-2011-301373. Epub 2012 May 6.

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