Recent Publications

Novel bacterial taxa in the human microbiome

Wylie, K. M. et al.

PLoS ONE (14 June 2012)

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants.

Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, Segata N, Morrow AL

Cell Rep 2016 Mar 29. PMID: 26997279

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 Feb 23. PMID: 26905627

Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria.

Abdelmaksoud AA, Koparde VN, Sheth NU, Serrano MG, Glascock AL, Fettweis JM, Strauss JF, Buck GA, Jefferson KK

Microbiology (Reading, Engl.) 2016 Feb . PMID: 26747455

High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis.

Simpson KE, Storch GA, Lee CK, Ward KE, Danon S, Simon CM, Delaney JW, Tong A, Canter CE

Pediatr Cardiol 2016 Feb . PMID: 26499513

Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma.

Neto AG, Whitaker A, Pei Z

Semin. Oncol. 2016 Feb . PMID: 26970127

Microbial community assembly and metabolic function during mammalian corpse decomposition.

Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R

Science 2016 Jan 8. PMID: 26657285

HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria.

Yang L, Poles MA, Fisch GS, Ma Y, Nossa C, Phelan JA, Pei Z

AIDS 2016 Jan 2. PMID: 26731752

Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production.

Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD

Gut 2016 Jan . PMID: 25431456

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 . PMID: 25394613

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma.

Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, Gaffney PM, Jervis LL, Cox D, Stephens L, Foster M, Tallbull G, Spicer P, Lewis CM

Curr. Biol. 2015 Dec 21. PMID: 26671671

Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri.

Gao C, Major A, Rendon D, Lugo M, Jackson V, Shi Z, Mori-Akiyama Y, Versalovic J

MBio 2015 . PMID: 26670383

Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts.

Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD

Inflamm. Bowel Dis. 2015 Dec . PMID: 26288001

Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season.

Wylie KM, Weinstock GM, Storch GA

J Pediatric Infect Dis Soc 2015 Dec . PMID: 26513823

The first microbial environment of infants born by C-section: the operating room microbes.

Shin H, Pei Z, Martinez KA, Rivera-Vinas JI, Mendez K, Cavallin H, Dominguez-Bello MG

Microbiome 2015 . PMID: 26620712

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease.

Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD

Cell Host Microbe 2015 Oct 14. PMID: 26468751

Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization.

Julian S, Burnham CA, Sellenriek P, Shannon WD, Hamvas A, Tarr PI, Warner BB

Infect Control Hosp Epidemiol 2015 Oct . PMID: 26108888

ConStrains identifies microbial strains in metagenomic datasets.

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D

Nat. Biotechnol. 2015 Oct . PMID: 26344404

Early life dynamics of the human gut virome and bacterial microbiome in infants.

Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR

Nat. Med. 2015 Oct . PMID: 26366711

Host genetic variation impacts microbiome composition across human body sites.

Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG

Genome Biol. 2015 . PMID: 26374288

Microbiome, a new dimension in cancer research.

Neto AG, Bradshaw AD, Pei Z

Ann Transl Med 2015 Sep . PMID: 26539446

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin.

Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H

ISME J 2015 Sep . PMID: 25848871

The gut microbiota in human energy homeostasis and obesity.

Rosenbaum M, Knight R, Leibel RL

Trends Endocrinol. Metab. 2015 Sep . PMID: 26257300

Structure and function of the healthy pre-adolescent pediatric gut microbiome.

Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta TA, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Shulman RJ, Versalovic J

Microbiome 2015 . PMID: 26306392

Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome.

Chumpitazi BP, Cope JL, Hollister EB, Tsai CM, McMeans AR, Luna RA, Versalovic J, Shulman RJ

Aliment. Pharmacol. Ther. 2015 Aug . PMID: 26104013

Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA.

Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H

Bioinformatics 2015 Aug 1. PMID: 25819674

Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease.

Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD

Inflamm. Bowel Dis. 2015 Aug . PMID: 26083617

Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease.

Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD

Inflamm. Bowel Dis. 2015 Aug . PMID: 25970545

mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis.

Davis C, Kota K, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wylie KM, Khetani R, Hudson ME, Weinstock GM, Mitreva M

J Data Mining Genomics Proteomics 2015 Aug . PMID: 26500804

Engineering the gut microbiota to treat hyperammonemia.

Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD

J. Clin. Invest. 2015 Jul 1. PMID: 26098218

Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis.

Segal LN, Blaser MJ

J. Pediatr. 2015 Jul . PMID: 25934071

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 . PMID: 25818499

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment.

Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ

Nat Commun 2015 . PMID: 26123276

Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis.

Kang D, Shi B, Erfe MC, Craft N, Li H

Sci Transl Med 2015 Jun 24. PMID: 26109103

Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response.

Ren W, Ma Y, Yang L, Gettie A, Salas J, Russell K, Blanchard J, Davidow A, Pei Z, Chang TL, Cheng-Mayer C

AIDS 2015 Jun 19. PMID: 26035329

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9.

Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD

MBio 2015 . PMID: 26081634

The cutaneous microbiome in outpatients presenting with acute skin abscesses.

Horton JM, Gao Z, Sullivan DM, Shopsin B, Perez-Perez GI, Blaser MJ

J. Infect. Dis. 2015 Jun 15. PMID: 25583170

Identifying personal microbiomes using metagenomic codes.

Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C

Proc. Natl. Acad. Sci. U.S.A. 2015 Jun 2. PMID: 25964341

Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection.

Allen-Daniels MJ, Serrano MG, Pflugner LP, Fettweis JM, Prestosa MA, Koparde VN, Brooks JP, Strauss JF, Romero R, Chaiworapongsa T, Eschenbach DA, Buck GA, Jefferson KK

Am. J. Obstet. Gynecol. 2015 Jun . PMID: 25637842

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism.

Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB

Cell Host Microbe 2015 May 13. PMID: 25891358

The preterm placental microbiome varies in association with excess maternal gestational weight gain.

Antony KM, Ma J, Mitchell KB, Racusin DA, Versalovic J, Aagaard K

Am. J. Obstet. Gynecol. 2015 May . PMID: 25557210

Diet in the pathogenesis and treatment of inflammatory bowel diseases.

Lee D, Albenberg L, Compher C, Baldassano R, Piccoli D, Lewis JD, Wu GD

Gastroenterology 2015 May . PMID: 25597840

New signaling pathways govern the host response to C. albicans infection in various niches.

Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM

Genome Res. 2015 May . PMID: 25858952

Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.

Huang EY, Inoue T, Leone VA, Dalal S, Touw K, Wang Y, Musch MW, Theriault B, Higuchi K, Donovan S, Gilbert J, Chang EB

Inflamm. Bowel Dis. 2015 May . PMID: 25738379

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification.

Vital M, Chai B, Østman B, Cole J, Konstantinidis KT, Tiedje JM

ISME J 2015 May . PMID: 25343512

The microbiome of uncontacted Amerindians.

Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG

Sci Adv 2015 Apr 3. PMID: 26229982

Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates.

Ma J, Purcell H, Showalter L, Aagaard KM

Am. J. Obstet. Gynecol. 2015 Apr . PMID: 25687567

'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics.

Harrison KL, Farrell RM, Brinich MA, Highland J, Mercer M, McCormick JB, Tilburt J, Geller G, Marshall P, Sharp RR

Health Expect 2015 Apr . PMID: 23279082

Subsistence strategies in traditional societies distinguish gut microbiomes.

Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM

Nat Commun 2015 . PMID: 25807110

Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia.

Vital M, Gao J, Rizzo M, Harrison T, Tiedje JM

ISME J 2015 Apr . PMID: 25343515

A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2.

Didion JP, Morgan AP, Clayshulte AM, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O'Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F

PLoS Genet. 2015 Feb . PMID: 25679959

The gut microbiome in health and in disease.

Shreiner AB, Kao JY, Young VB

Curr. Opin. Gastroenterol. 2015 Jan . PMID: 25394236

Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease.

Vital M, Harkema JR, Rizzo M, Tiedje J, Brandenberger C

J Immunol Res 2015 . PMID: 26090504

Microfluidic Flow Cytometry for Single-Cell Protein Analysis.

Wu M, Singh AK

Methods Mol. Biol. 2015 . PMID: 26542716

Lungs, microbes and the developing neonate.

Warner BB, Hamvas A

Neonatology 2015 . PMID: 26044101

A RESTful API for accessing microbial community data for MG-RAST.

Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F

PLoS Comput. Biol. 2015 Jan . PMID: 25569221

Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants.

Taft DH, Ambalavanan N, Schibler KR, Yu Z, Newburg DS, Deshmukh H, Ward DV, Morrow AL

PLoS ONE 2015 . PMID: 26110908

Sex, body mass index, and dietary fiber intake influence the human gut microbiome.

Dominianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, Ahn J

PLoS ONE 2015 . PMID: 25874569

Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study.

Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE

PLoS ONE 2015 . PMID: 25741698

Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems.

Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK

Lab Chip 2014 Dec 7. PMID: 25270338

Beyond infectious disease: welcome to the era of population microbiology.

Pincus MR, Pei Z

Clin. Lab. Med. 2014 Dec . PMID: 25439278

The changing landscape of the vaginal microbiome.

Huang B, Fettweis JM, Brooks JP, Jefferson KK, Buck GA

Clin. Lab. Med. 2014 Dec . PMID: 25439274

Microbiome, innate immunity, and esophageal adenocarcinoma.

Baghdadi J, Chaudhary N, Pei Z, Yang L

Clin. Lab. Med. 2014 Dec . PMID: 25439272

The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis.

Cho M, Carter J, Harari S, Pei Z

Clin. Lab. Med. 2014 Dec . PMID: 25439270

Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.

Zhou Y, Burnham CA, Hink T, Chen L, Shaikh N, Wollam A, Sodergren E, Weinstock GM, Tarr PI, Dubberke ER

J. Clin. Microbiol. 2014 Dec . PMID: 25275005

Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection.

Brotman RM, Shardell MD, Gajer P, Tracy JK, Zenilman JM, Ravel J, Gravitt PE

J. Infect. Dis. 2014 Dec 1. PMID: 24943724

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA

BMC Bioinformatics 2014 . PMID: 25407910

Evolution of invasion in a diverse set of Fusobacterium species.

Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM

MBio 2014 . PMID: 25370491

An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women.

Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L, Fajans M, Anderson ME, Jaoko W, Kurth AE

AIDS Res. Hum. Retroviruses 2014 Nov . PMID: 25265254

Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD

Gastroenterology 2014 Nov . PMID: 25046162

High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis.

Smallwood TL, Gatti DM, Quizon P, Weinstock GM, Jung KC, Zhao L, Hua K, Pomp D, Bennett BJ

G3 (Bethesda) 2014 Dec . PMID: 25344410

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, White O

Cell 2014 Oct 9. PMID: 25303518

Biogeography and individuality shape function in the human skin metagenome.

Oh J, Byrd AL, Deming C, Conlan S, Kong HH, Segre JA

Nature 2014 Oct 2. PMID: 25279917

The microbiome revolution.

Blaser MJ

J. Clin. Invest. 2014 Oct . PMID: 25271724

Differences in vaginal microbiome in African American women versus women of European ancestry.

Fettweis JM, Brooks JP, Serrano MG, Sheth NU, Girerd PH, Edwards DJ, Strauss JF, Jefferson KK, Buck GA

Microbiology (Reading, Engl.) 2014 Oct . PMID: 25073854

From deep sequencing to actual clones.

D'Angelo S, Kumar S, Naranjo L, Ferrara F, Kiss C, Bradbury AR

Protein Eng. Des. Sel. 2014 Oct . PMID: 25183780

Metagenomic analysis of double-stranded DNA viruses in healthy adults.

Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM

BMC Biol. 2014 . PMID: 25212266

DRISEE overestimates errors in metagenomic sequencing data.

Eren AM, Morrison HG, Huse SM, Sogin ML

Brief. Bioinformatics 2014 Sep . PMID: 23698723

Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota.

Campbell AG, Schwientek P, Vishnivetskaya T, Woyke T, Levy S, Beall CJ, Griffen A, Leys E, Podar M

Environ. Microbiol. 2014 Sep . PMID: 24738594

CcpA is important for growth and virulence of Enterococcus faecium.

Somarajan SR, Roh JH, Singh KV, Weinstock GM, Murray BE

Infect. Immun. 2014 Sep . PMID: 24914215

Longitudinal analysis of microbial interaction between humans and the indoor environment.

Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA

Science 2014 Aug 29. PMID: 25170151

Patterned progression of bacterial populations in the premature infant gut.

La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE, Shaikh N, Linneman LA, Hoffmann JA, Hamvas A, Deych E, Shands BA, Shannon WD, Tarr PI

Proc. Natl. Acad. Sci. U.S.A. 2014 Aug 26. PMID: 25114261

Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium.

Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS

Int. J. Syst. Evol. Microbiol. 2014 Aug . PMID: 24824639

Oligotyping analysis of the human oral microbiome.

Eren AM, Borisy GG, Huse SM, Mark Welch JL

Proc. Natl. Acad. Sci. U.S.A. 2014 Jul 15. PMID: 24965363

Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt.

Lee SC, Billmyre RB, Li A, Carson S, Sykes SM, Huh EY, Mieczkowski P, Ko DC, Cuomo CA, Heitman J

MBio 2014 . PMID: 25006230

Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells.

Boonma P, Spinler JK, Venable SF, Versalovic J, Tumwasorn S

BMC Microbiol. 2014 . PMID: 24989059

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK

ISME J 2014 Jul . PMID: 24451203

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition.

Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, Kotloff K, Ikumapayi UN, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, Morris JG, Breiman RF, Saha D, Parkhill J, Nataro JP, Stine OC

Genome Biol. 2014 . PMID: 24995464

From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions.

Spinler JK, Sontakke A, Hollister EB, Venable SF, Oh PL, Balderas MA, Saulnier DM, Mistretta TA, Devaraj S, Walter J, Versalovic J, Highlander SK

Genome Biol Evol 2014 Jul . PMID: 24951561

Finding the missing links among metabolites, microbes, and the host.

Dorrestein PC, Mazmanian SK, Knight R

Immunity 2014 Jun 19. PMID: 24950202

Evidence of extensive DNA transfer between bacteroidales species within the human gut.

Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE

MBio 2014 . PMID: 24939888

Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251).

Cuomo CA, Rodriguez-Del Valle N, Perez-Sanchez L, Abouelleil A, Goldberg J, Young S, Zeng Q, Birren BW

Genome Announc 2014 . PMID: 24855299

The placenta harbors a unique microbiome.

Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J

Sci Transl Med 2014 May 21. PMID: 24848255

Exploration of bacterial community classes in major human habitats.

Zhou Y, Mihindukulasuriya KA, Gao H, La Rosa PS, Wylie KM, Martin JC, Kota K, Shannon WD, Mitreva M, Sodergren E, Weinstock GM

Genome Biol. 2014 . PMID: 24887286

Microbiome in reflux disorders and esophageal adenocarcinoma.

Yang L, Chaudhary N, Baghdadi J, Pei Z

Cancer J . PMID: 24855009

Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections.

Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR, Johnston BD, Burnham CA, Weinstock ES, Weinstock GM, Wylie TN, Mitreva M, Abubucker S, Zhou Y, Stevens HJ, Hall-Moore C, Julian S, Shaikh N, Warner BB, Tarr PI

Clin. Infect. Dis. 2014 May . PMID: 24647013

Compositional and functional features of the gastrointestinal microbiome and their effects on human health.

Hollister EB, Gao C, Versalovic J

Gastroenterology 2014 May . PMID: 24486050

Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.

Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z

J. Virol. 2014 May . PMID: 24522917

Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy.

Brotman RM, Shardell MD, Gajer P, Fadrosh D, Chang K, Silver MI, Viscidi RP, Burke AE, Ravel J, Gravitt PE

Menopause 2014 May . PMID: 24080849

Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.

Vital M, Howe AC, Tiedje JM

MBio 2014 . PMID: 24757212

Transferable vancomycin resistance in a community-associated MRSA lineage.

Rossi F, Diaz L, Wollam A, Panesso D, Zhou Y, Rincon S, Narechania A, Xing G, Di Gioia TS, Doi A, Tran TT, Reyes J, Munita JM, Carvajal LP, Hernandez-Roldan A, Brandão D, van der Heijden IM, Murray BE, Planet PJ, Weinstock GM, Arias CA

N. Engl. J. Med. 2014 Apr 17. PMID: 24738669

Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.

Chen Z, Martinez DA, Gujja S, Sykes SM, Zeng Q, Szaniszlo PJ, Wang Z, Cuomo CA

G3 (Bethesda) 2014 Apr . PMID: 24496724

Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma.

Xu W, Yang L, Lee P, Huang WC, Nossa C, Ma Y, Deng FM, Zhou M, Melamed J, Pei Z

Am J Clin Exp Urol 2014 Apr 15. PMID: 25126590

Antibacterial property expressed by a novel calcium phosphate glass.

Liu L, Pushalkar S, Saxena D, LeGeros RZ, Zhang Y

J. Biomed. Mater. Res. Part B Appl. Biomater. 2014 Apr . PMID: 24039127

Pathogens and host immunity in the ancient human oral cavity.

Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Collins MJ, Gilbert MT, Rühli F, Cappellini E

Nat. Genet. 2014 Apr . PMID: 24562188

Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production.

Hemarajata P, Spinler JK, Balderas MA, Versalovic J

Antonie Van Leeuwenhoek 2014 Mar . PMID: 24488273

Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome.

Chumpitazi BP, Hollister EB, Oezguen N, Tsai CM, McMeans AR, Luna RA, Savidge TC, Versalovic J, Shulman RJ

Gut Microbes . PMID: 24637601

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.

Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J

Microbiome 2014 . PMID: 24558975

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 . PMID: 24529162

A brave new world: the lung microbiota in an era of change.

Segal LN, Blaser MJ

Ann Am Thorac Soc 2014 Jan . PMID: 24437400

Probiotics: achieving a better regulatory fit.

Hoffmann DE, Fraser CM, Palumbo F, Ravel J, Rowthorn V, Schwartz J

Food Drug Law J 2014 . PMID: 25163211

BOTUX: bayesian-like operational taxonomic unit examiner.

Koparde VN, Adkins RS, Fettweis JM, Serrano MG, Buck GA, Reimers MA, Sheth NU

Int J Comput Biol Drug Des 2014 . PMID: 24878725

MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH.

Wu M, Piccini ME, Singh AK

Methods Mol. Biol. 2014 . PMID: 25218391

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 . PMID: 25071935

Ribosomal Database Project: data and tools for high throughput rRNA analysis.

Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM

Nucleic Acids Res. 2014 Jan . PMID: 24288368

MetaRef: a pan-genomic database for comparative and community microbial genomics.

Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N

Nucleic Acids Res. 2014 Jan . PMID: 24203705

IMG/M 4 version of the integrated metagenome comparative analysis system.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC

Nucleic Acids Res. 2014 Jan . PMID: 24136997

An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease.

Fettweis JM, Serrano MG, Huang B, Brooks JP, Glascock AL, Sheth NU, Strauss JF, Jefferson KK, Buck GA

PLoS ONE 2014 . PMID: 25337710

The prevalence of species and strains in the human microbiome: a resource for experimental efforts.

Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M

PLoS ONE 2014 . PMID: 24827833

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.

Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland ED, Harris CC, Sczyrba A, Chain PS, Koren S, Woyke T, Stepanauskas R

PLoS ONE 2014 . PMID: 24743558

Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis.

Hyde ER, Andrade F, Vaksman Z, Parthasarathy K, Jiang H, Parthasarathy DK, Torregrossa AC, Tribble G, Kaplan HB, Petrosino JF, Bryan NS

PLoS ONE 2014 . PMID: 24670812

History and impact of RDP: a legacy from Carl Woese to microbiology.

Cole JR, Tiedje JM

RNA Biol 2014 . PMID: 24607969

Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis.

Ravel J, Brotman RM, Gajer P, Ma B, Nandy M, Fadrosh DW, Sakamoto J, Koenig SS, Fu L, Zhou X, Hickey RJ, Schwebke JR, Forney LJ

Microbiome 2013 . PMID: 24451163

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies.

Oh J, Freeman AF, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH

Genome Res. 2013 Dec . PMID: 24170601

Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri.

Hemarajata P, Gao C, Pflughoeft KJ, Thomas CM, Saulnier DM, Spinler JK, Versalovic J

J. Bacteriol. 2013 Dec . PMID: 24123819

Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.

Turabelidze G, Lawrence SJ, Gao H, Sodergren E, Weinstock GM, Abubucker S, Wylie T, Mitreva M, Shaikh N, Gautom R, Tarr PI

J. Clin. Microbiol. 2013 Dec . PMID: 24048526

Microfluidic platforms for single-cell protein analysis.

Liu Y, Singh AK

J Lab Autom 2013 Dec . PMID: 23821679

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. PMID: 24358444

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.

Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K

Nat. Biotechnol. 2013 Dec . PMID: 24213699

Differential abundance analysis for microbial marker-gene surveys.

Paulson JN, Stine OC, Bravo HC, Pop M

Nat. Methods 2013 Dec . PMID: 24076764

Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes.

Close DW, Ferrara F, Dichosa AE, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury AR

BMC Microbiol. 2013 . PMID: 24279426

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.

Wendl MC, Kota K, Weinstock GM, Mitreva M

J Math Biol 2013 Nov . PMID: 22965653

Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue.

Huang EY, Leone VA, Devkota S, Wang Y, Brady MJ, Chang EB

JPEN J Parenter Enteral Nutr 2013 Nov . PMID: 23639897

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 . PMID: 24451123

Science and regulation. Probiotics: finding the right regulatory balance.

Hoffmann DE, Fraser CM, Palumbo FB, Ravel J, Rothenberg K, Rowthorn V, Schwartz J

Science 2013 Oct 18. PMID: 24136953

Interprovider variation of celiac disease testing in childhood chronic abdominal pain.

Chumpitazi BP, Mysore K, Tsai CM, Shulman RJ

BMC Gastroenterol 2013 . PMID: 24124697

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD

Appl. Environ. Microbiol. 2013 Sep . PMID: 23793624

Propionibacterium acnes strain populations in the human skin microbiome associated with acne.

Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H

J. Invest. Dermatol. 2013 Sep . PMID: 23337890

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C

Nat. Biotechnol. 2013 Sep . PMID: 23975157

Association of gut microbiota with post-operative clinical course in Crohn's disease.

Dey N, Soergel DA, Repo S, Brenner SE

BMC Gastroenterol 2013 . PMID: 23964800

De novo likelihood-based measures for comparing genome assemblies.

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M

BMC Res Notes 2013 . PMID: 23965294

Virome genomics: a tool for defining the human virome.

Wylie KM, Weinstock GM, Storch GA

Curr. Opin. Microbiol. 2013 Aug . PMID: 23706900

Rapid evolution of the human gut virome.

Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD

Proc. Natl. Acad. Sci. U.S.A. 2013 Jul 23. PMID: 23836644

Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review.

Hale CS, Huang H, Melamed J, Xu R, Roberts L, Wieczorek R, Pei Z, Lee P

Int J Clin Exp Pathol 2013 . PMID: 23923086

Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients.

Melamed R, Storch GA, Warner BB, Tarr PI

Arch. Dis. Child. Fetal Neonatal Ed. 2013 Jul . PMID: 23563694

Analysis of the human gut microbiome and association with disease.

Wu GD, Lewis JD

Clin. Gastroenterol. Hepatol. 2013 Jul . PMID: 23643636

Colitis-induced bone loss is gender dependent and associated with increased inflammation.

Irwin R, Lee T, Young VB, Parameswaran N, McCabe LR

Inflamm. Bowel Dis. 2013 Jul . PMID: 23702805

Topographic diversity of fungal and bacterial communities in human skin.

Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, Kong HH, Segre JA

Nature 2013 Jun 20. PMID: 23698366

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 . PMID: 23799126

Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.

Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD

PLoS ONE 2013 . PMID: 23799070

Sequencing viral genomes from a single isolated plaque.

Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE

Virol. J. 2013 . PMID: 23742765

Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.

Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, Li JZ, LiPuma JJ

Ann Am Thorac Soc 2013 Jun . PMID: 23802813

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M

Environ. Microbiol. 2013 Jun . PMID: 23387867

Analyses of the stability and core taxonomic memberships of the human microbiome.

Li K, Bihan M, Methé BA

PLoS ONE 2013 . PMID: 23671663

A Pure L1-norm Principal Component Analysis.

Brooks J, Dulá J, Boone E

Comput Stat Data Anal 2013 May 1. PMID: 23976807

The future is now: single-cell genomics of bacteria and archaea.

Blainey PC

FEMS Microbiol. Rev. 2013 May . PMID: 23298390

Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.

Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS

Genome Res. 2013 May . PMID: 23493677

Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.

Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL

Nat. Med. 2013 May . PMID: 23563705

Cohabiting family members share microbiota with one another and with their dogs.

Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R

Elife 2013 . PMID: 23599893

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.

Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M

Proc. Natl. Acad. Sci. U.S.A. 2013 Apr 2. PMID: 23509275

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.

Chen J, Bushman FD, Lewis JD, Wu GD, Li H

Biostatistics 2013 Apr . PMID: 23074263

The human gut microbiome and body metabolism: implications for obesity and diabetes.

Devaraj S, Hemarajata P, Versalovic J

Clin. Chem. 2013 Apr . PMID: 23401286

Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.

Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ

J. Infect. Dis. 2013 Apr . PMID: 23300163

SPA: a short peptide assembler for metagenomic data.

Yang Y, Yooseph S

Nucleic Acids Res. 2013 Apr . PMID: 23435317

Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling.

Wu X, Berkow K, Frank DN, Li E, Gulati AS, Zhu W

BMC Bioinformatics 2013 . PMID: 23497007

Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.

Ursell LK, Knight R

Cell Metab. 2013 Mar 5. PMID: 23473028

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 . PMID: 24451366

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 . PMID: 24451334

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M

Brief. Bioinformatics 2013 Mar . PMID: 22199379

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.

Aagaard K, Petrosino J, Keitel W, Watson M, Katancik J, Garcia N, Patel S, Cutting M, Madden T, Hamilton H, Harris E, Gevers D, Simone G, McInnes P, Versalovic J

FASEB J. 2013 Mar . PMID: 23165986

Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda.

Denson LA, Long MD, McGovern DP, Kugathasan S, Wu GD, Young VB, Pizarro TT, de Zoeten EF, Stappenbeck TS, Plevy SE, Abraham C, Nusrat A, Jobin C, McCole DF, Siegel CA, Higgins PD, Herfarth HH, Hyams J, Sandborn WJ, Loftus EV, Kappelman MD, Lewis JD, Parkos CA, Sartor RB

Inflamm. Bowel Dis. . PMID: 23448796

Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.

Leone V, Chang EB, Devkota S

J. Gastroenterol. 2013 Mar . PMID: 23475322

Shallow breathing: bacterial life at low O(2).

Morris RL, Schmidt TM

Nat. Rev. Microbiol. 2013 Mar . PMID: 23411864

Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.

Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT

Chem. Biol. 2013 Jan 24. PMID: 23352146

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M

Genome Biol. 2013 . PMID: 23320958

Biogeography of the ecosystems of the healthy human body.

Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM

Genome Biol. 2013 . PMID: 23316946

An analysis of online messages about probiotics.

Brinich MA, Mercer MB, Sharp RR

BMC Gastroenterol 2013 . PMID: 23311418

Genomic variation landscape of the human gut microbiome.

Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P

Nature 2013 Jan 3. PMID: 23222524

Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy.

Tran TT, Panesso D, Gao H, Roh JH, Munita JM, Reyes J, Diaz L, Lobos EA, Shamoo Y, Mishra NN, Bayer AS, Murray BE, Weinstock GM, Arias CA

Antimicrob. Agents Chemother. 2013 Jan . PMID: 23114757

Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain.

Kasimatis G, Fitz-Gibbon S, Tomida S, Wong M, Li H

Biomed Res Int 2013 . PMID: 23762865

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.

Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R

ISME J 2013 Jan . PMID: 22895161

Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice.

Bhattacharyya S, Xue L, Devkota S, Chang E, Morris S, Tobacman JK

Mediators Inflamm. 2013 . PMID: 23766559

A metagenomics portal for a democratized sequencing world.

Wilke A, Glass EM, Bartels D, Bischof J, Braithwaite D, D'Souza M, Gerlach W, Harrison T, Keegan K, Matthews H, Kottmann R, Paczian T, Tang W, Trimble WL, Yilmaz P, Wilkening J, Desai N, Meyer F

Meth. Enzymol. 2013 . PMID: 24060134

Optofluidic cell selection from complex microbial communities for single-genome analysis.

Landry ZC, Giovanonni SJ, Quake SR, Blainey PC

Meth. Enzymol. 2013 . PMID: 24060116

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.

Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG

Nat. Methods 2013 Jan . PMID: 23202435

Diet, gut enterotypes and health: is there a link?

Bushman FD, Lewis JD, Wu GD

Nestle Nutr Inst Workshop Ser 2013 . PMID: 24107497

TIGRFAMs and Genome Properties in 2013.

Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E

Nucleic Acids Res. 2013 Jan . PMID: 23197656

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE

PLoS Comput. Biol. 2013 . PMID: 23326225

Diversified microbiota of meconium is affected by maternal diabetes status.

Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H, Peter I

PLoS ONE 2013 . PMID: 24223144

Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment.

Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD

PLoS ONE 2013 . PMID: 23977147

Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity.

Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M

PLoS ONE 2013 . PMID: 23555659

Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk.

Munch EM, Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K

PLoS ONE 2013 . PMID: 23418415

Single cell microRNA analysis using microfluidic flow cytometry.

Wu M, Piccini M, Koh CY, Lam KS, Singh AK

PLoS ONE 2013 . PMID: 23383050

Investigators' perspectives on translating human microbiome research into clinical practice.

Slashinski MJ, Whitney SN, Achenbaum LS, Keitel WA, McCurdy SA, McGuire AL

Public Health Genomics 2013 . PMID: 23615375

Microbiomic signatures of psoriasis: feasibility and methodology comparison.

Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF

Sci Rep 2013 . PMID: 24018484

Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.

Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ

J. Bacteriol. 2012 Dec . PMID: 23209255

Detection of viruses in young children with fever without an apparent source.

Colvin JM, Muenzer JT, Jaffe DM, Smason A, Deych E, Shannon WD, Arens MQ, Buller RS, Lee WM, Weinstock EJ, Weinstock GM, Storch GA

Pediatrics 2012 Dec . PMID: 23129086

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R

Curr Protoc Microbiol 2012 Nov . PMID: 23184592

Host genetic and environmental effects on mouse intestinal microbiota.

Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M

ISME J 2012 Nov . PMID: 22695862

Dietary issues in recurrent abdominal pain.

Shulman RJ

J. Pediatr. Gastroenterol. Nutr. 2012 Nov . PMID: 23103654

"Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research.

Slashinski MJ, McCurdy SA, Achenbaum LS, Whitney SN, McGuire AL

BMC Med Ethics 2012 . PMID: 23110633

Diversity of 5S rRNA genes within individual prokaryotic genomes.

Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z

FEMS Microbiol. Lett. 2012 Oct . PMID: 22765222

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts.

Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R

Genome Res. 2012 Oct . PMID: 22665442

Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women.

Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J

Sex Transm Dis 2012 Oct . PMID: 23007708

Emerging view of the human virome.

Wylie KM, Weinstock GM, Storch GA

Transl Res 2012 Oct . PMID: 22683423

Understanding vaginal microbiome complexity from an ecological perspective.

Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ

Transl Res 2012 Oct . PMID: 22683415

The microbiome of the lung.

Beck JM, Young VB, Huffnagle GB

Transl Res 2012 Oct . PMID: 22683412

Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.

Blainey PC, Milla CE, Cornfield DN, Quake SR

Sci Transl Med 2012 Sep 26. PMID: 23019655

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.

Wu YW, Rho M, Doak TG, Ye Y

Bioinformatics 2012 Sep 15. PMID: 22962453

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.

Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF

Cell Host Microbe 2012 Sep 13. PMID: 22980325

Genomic approaches to studying the human microbiota.

Weinstock GM

Nature 2012 Sep 13. PMID: 22972298

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 . PMID: 22753064

Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice.

Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Barrish JP, Finegold MJ, Petrosino JF, Guerrant RL, Conner ME, Versalovic J

J. Pediatr. Gastroenterol. Nutr. 2012 Sep . PMID: 22343914

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 . PMID: 22911969

Associating microbiome composition with environmental covariates using generalized UniFrac distances.

Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H

Bioinformatics 2012 Aug 15. PMID: 22711789

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z

Bioinformatics 2012 Aug 15. PMID: 22692220

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R

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Defining the human microbiome.

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Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.

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Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates.

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Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma.

Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D

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Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.

Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE

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Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.

Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB

Nature 2012 Jul 5. PMID: 22722865

A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples.

Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD

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Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy.

Harrison KL, Geller G, Marshall P, Tilburt J, Mercer M, Brinich MA, Highland J, Farrell RM, Sharp RR

AJOB Prim Res 2012 Jul 1. PMID: 22773953

Spatial and temporal variability of the human microbiota.

Parfrey LW, Knight R

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Food and the gut microbiota in inflammatory bowel diseases: a critical connection.

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Stabilization of the murine gut microbiome following weaning.

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Soergel DA, Dey N, Knight R, Brenner SE

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Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.

Wang X, Cai Y, Sun Y, Knight R, Mai V

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Perspectives on human microbiome research ethics.

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J Empir Res Hum Res Ethics 2012 Jul . PMID: 22850139

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples.

Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J

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A framework for human microbiome research.

Nature 2012 Jun 14. PMID: 22699610

Unlocking the potential of metagenomics through replicated experimental design.

Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA

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'Omics' of the mammalian gut--new insights into function.

Lamendella R, VerBerkmoes N, Jansson JK

Curr. Opin. Biotechnol. 2012 Jun . PMID: 22626866

Single cell genome sequencing.

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Characterizing microbial communities through space and time.

Gonzalez A, King A, Robeson MS, Song S, Shade A, Metcalf JL, Knight R

Curr. Opin. Biotechnol. 2012 Jun . PMID: 22154467

Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).

Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC

Genome Res. 2012 Jun . PMID: 22434425

Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.

Ozok AR, Persoon IF, Huse SM, Keijser BJ, Wesselink PR, Crielaard W, Zaura E

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Temporal dynamics of the human vaginal microbiota.

Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J

Sci Transl Med 2012 May 2. PMID: 22553250

A new era of the vaginal microbiome: advances using next-generation sequencing.

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Chem. Biodivers. 2012 May . PMID: 22589096

Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine.

Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J

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Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.

Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Murray PR, Turner ML, Segre JA

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The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.

Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R

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Significance of the microbiome in obstructive lung disease.

Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ

Thorax 2012 May . PMID: 22318161

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C

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Decade-long bacterial community dynamics in cystic fibrosis airways.

Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ

Proc. Natl. Acad. Sci. U.S.A. 2012 Apr 10. PMID: 22451929

Responses of gut microbiota to diet composition and weight loss in lean and obese mice.

Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL

Obesity (Silver Spring) 2012 Apr . PMID: 21593810

Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation.

Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D, Kubo M, Kambayashi T, Larosa DF, Renner ED, Orange JS, Bushman FD, Artis D

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AntiFam: a tool to help identify spurious ORFs in protein annotation.

Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A

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The human microbiome: at the interface of health and disease.

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Experiences of patients with chronic gastrointestinal conditions: in their own words.

McCormick JB, Hammer RR, Farrell RM, Geller G, James KM, Loftus EV, Mercer MB, Tilburt JC, Sharp RR

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Hypervariable loci in the human gut virome.

Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD

Proc. Natl. Acad. Sci. U.S.A. 2012 Mar 6. PMID: 22355105

Human microbiome and HIV/AIDS.

Saxena D, Li Y, Yang L, Pei Z, Poles M, Abrams WR, Malamud D

Curr HIV/AIDS Rep 2012 Mar . PMID: 22193889

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA

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Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis.

Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M, Gewirtz AT

Gut 2012 Mar . PMID: 21646247

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P

ISME J 2012 Mar . PMID: 22134646

Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice.

Mei J, Liu Y, Dai N, Hoffmann C, Hudock KM, Zhang P, Guttentag SH, Kolls JK, Oliver PM, Bushman FD, Worthen GS

J. Clin. Invest. 2012 Mar . PMID: 22326959

SitePainter: a tool for exploring biogeographical patterns.

Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R

Bioinformatics 2012 Feb 1. PMID: 22171330

Single-cell protein analysis.

Wu M, Singh AK

Curr. Opin. Biotechnol. 2012 Feb . PMID: 22189001

Advancing analytical algorithms and pipelines for billions of microbial sequences.

Gonzalez A, Knight R

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The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

He Z, Piceno Y, Deng Y, Xu M, Lu Z, Desantis T, Andersen G, Hobbie SE, Reich PB, Zhou J

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How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome.

Mercer M, Brinich MA, Geller G, Harrison K, Highland J, James K, Marshall P, McCormick JB, Tilburt J, Achkar JP, Farrell RM, Sharp RR

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Vaginal microbiome: rethinking health and disease.

Ma B, Forney LJ, Ravel J

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The L1-norm best-fit hyperplane problem.

Brooks JP, Dulá JH

Appl Math Lett 2012 Jan 1. PMID: 23024460

Epigenetic priors for identifying active transcription factor binding sites.

Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL

Bioinformatics 2012 Jan 1. PMID: 22072382

Graph accordance of next-generation sequence assemblies.

Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM

Bioinformatics 2012 Jan 1. PMID: 22025481

The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.

Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A

BMC Bioinformatics 2012 . PMID: 23320832

Species-level classification of the vaginal microbiome.

Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, Brooks JP, Jefferson KK, Buck GA

BMC Genomics 2012 . PMID: 23282177

Genomic sequence analysis and characterization of Sneathia amnii sp. nov.

Harwich MD, Serrano MG, Fettweis JM, Alves JM, Reimers MA, Buck GA, Jefferson KK

BMC Genomics 2012 . PMID: 23281612

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.

Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V

Brief. Bioinformatics 2012 Jan . PMID: 21525143

The intestinal microbiota in health and disease.

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Curr. Opin. Gastroenterol. 2012 Jan . PMID: 22080827

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A

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Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.

Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE

ISME J 2012 Jan . PMID: 21716311

IMG: the Integrated Microbial Genomes database and comparative analysis system.

Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC

Nucleic Acids Res. 2012 Jan . PMID: 22194640

CharProtDB: a database of experimentally characterized protein annotations.

Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D

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The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.

Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC

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IMG/M: the integrated metagenome data management and comparative analysis system.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC

Nucleic Acids Res. 2012 Jan . PMID: 22086953

Antibiotic effects on bacterial profile in osteonecrosis of the jaw.

Ji X, Pushalkar S, Li Y, Glickman R, Fleisher K, Saxena D

Oral Dis 2012 Jan . PMID: 21883710

The Human Microbiome Project: a community resource for the healthy human microbiome.

Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C

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Bioinformatics for the Human Microbiome Project.

Gevers D, Pop M, Schloss PD, Huttenhower C

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Microbial co-occurrence relationships in the human microbiome.

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Metabolic reconstruction for metagenomic data and its application to the human microbiome.

Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C

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Diverse CRISPRs evolving in human microbiomes.

Rho M, Wu YW, Tang H, Doak TG, Ye Y

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Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism.

Pathak DT, Wei X, Bucuvalas A, Haft DH, Gerloff DL, Wall D

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Hypothesis testing and power calculations for taxonomic-based human microbiome data.

La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD

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Insights from characterizing extinct human gut microbiomes.

Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM

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Increased prevalence of anellovirus in pediatric patients with fever.

McElvania TeKippe E, Wylie KM, Deych E, Sodergren E, Weinstock G, Storch GA

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Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.

Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK

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Statistical object data analysis of taxonomic trees from human microbiome data.

La Rosa PS, Shands B, Deych E, Zhou Y, Sodergren E, Weinstock G, Shannon WD

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Estimation of distribution overlap of urn models.

Hampton J, Lladser ME

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Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.

Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M

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Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.

Conlan S, Kong HH, Segre JA

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Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile.

Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, Zhu J, Bushman FD

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Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.

Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM

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Conservation of gene cassettes among diverse viruses of the human gut.

Minot S, Wu GD, Lewis JD, Bushman FD

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The "most wanted" taxa from the human microbiome for whole genome sequencing.

Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM

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IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.

Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC

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A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.

Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J

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Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.

Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M

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Novel bacterial taxa in the human microbiome.

Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS

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A core human microbiome as viewed through 16S rRNA sequence clusters.

Huse SM, Ye Y, Zhou Y, Fodor AA

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Analyses of the microbial diversity across the human microbiome.

Li K, Bihan M, Yooseph S, Methé BA

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Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

Zhang T, DeSimone RA, Jiao X, Rohlf FJ, Zhu W, Gong QQ, Hunt SR, Dassopoulos T, Newberry RD, Sodergren E, Weinstock G, Robertson CE, Frank DN, Li E

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A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA

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Complex carbohydrate utilization by the healthy human microbiome.

Cantarel BL, Lombard V, Henrissat B

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Sequence analysis of the human virome in febrile and afebrile children.

Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA

PLoS ONE 2012 . PMID: 22719819

Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.

Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, Zhang T, Rohlf FJ, Zhu W, Gu C, Robertson CE, Pace NR, Boedeker EC, Harpaz N, Yuan J, Weinstock GM, Sodergren E, Frank DN

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Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S

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Comparison of storage conditions for human vaginal microbiome studies.

Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM

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An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies.

Zhang T, Song B, Zhu W, Xu X, Gong QQ, Morando C, Dassopoulos T, Newberry RD, Hunt SR, Li E

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Bacterial communities of the coronal sulcus and distal urethra of adolescent males.

Nelson DE, Dong Q, Van der Pol B, Toh E, Fan B, Katz BP, Mi D, Rong R, Weinstock GM, Sodergren E, Fortenberry JD

PLoS ONE 2012 . PMID: 22606251

Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon.

Harrell L, Wang Y, Antonopoulos D, Young V, Lichtenstein L, Huang Y, Hanauer S, Chang E

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Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Thompson JD, Shibahara G, Rajan S, Pel J, Marziali A

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The Jeremiah Metzger Lecture: Global warming redux: the disappearing microbiota and epidemic obesity.

Blaser MJ

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The Human Microbiome Project: lessons from human genomics.

Lewis CM, Obregón-Tito A, Tito RY, Foster MW, Spicer PG

Trends Microbiol. 2012 Jan . PMID: 22112388

Experimental and analytical tools for studying the human microbiome.

Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R

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Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.

Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C

Bioinformatics 2011 Dec 1. PMID: 21984758

Using QIIME to analyze 16S rRNA gene sequences from microbial communities.

Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R

Curr Protoc Bioinformatics 2011 Dec . PMID: 22161565

Saying privacy, meaning confidentiality.

Schwab AP, Frank L, Gligorov N

Am J Bioeth 2011 Nov . PMID: 22047127

De minimis risk: a proposal for a new category of research risk.

Rhodes R, Azzouni J, Baumrin SB, Benkov K, Blaser MJ, Brenner B, Dauben JW, Earle WJ, Frank L, Gligorov N, Goldfarb J, Hirschhorn K, Hirschhorn R, Holzman I, Indyk D, Jabs EW, Lackey DP, Moros DA, Philpott S, Rhodes ME, Richardson LD, Sacks HS, Schwab A, Sperling R, Trusko B, Zweig A

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Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).

Youssef NH, Blainey PC, Quake SR, Elshahed MS

Appl. Environ. Microbiol. 2011 Nov . PMID: 21908640

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M

Bioinformatics 2011 Nov 1. PMID: 21926123

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.

Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R

Bioinformatics 2011 Nov 1. PMID: 21903626

Astrovirus MLB2 viremia in febrile child.

Holtz LR, Wylie KM, Sodergren E, Jiang Y, Franz CJ, Weinstock GM, Storch GA, Wang D

Emerging Infect. Dis. 2011 Nov . PMID: 22099095

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J

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Microbiome and malignancy.

Plottel CS, Blaser MJ

Cell Host Microbe 2011 Oct 20. PMID: 22018233

Human-associated microbial signatures: examining their predictive value.

Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R

Cell Host Microbe 2011 Oct 20. PMID: 22018228

Linking long-term dietary patterns with gut microbial enterotypes.

Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD

Science 2011 Oct 7. PMID: 21885731

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.

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Building a comprehensive genomic program for hepatocellular carcinoma.

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Boulder ALignment Editor (ALE): a web-based RNA alignment tool.

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