Publications

Strains, functions and dynamics in the expanded Human Microbiome Project.

Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C

Nature 2017 10 05. PMID: 28953883

A New Catalog of Microbiological Tools for Women's Infectious Disease Research.

Lewis AL, Lewis WG

Genome Announc 2016 Sep 29. PMID: 27688331

Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates.

Deitzler GE, Ruiz MJ, Lu W, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL

Genome Announc 2016 Sep 29. PMID: 27688330

Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina.

Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson L, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis AL, Lewis WG

Genome Announc 2016 Sep 29. PMID: 27688329

Genome Sequences of 11 Human Vaginal Actinobacteria Strains.

Lewis AL, Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG

Genome Announc 2016 Sep 29. PMID: 27688328

Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women.

Weimer CM, Deitzler GE, Robinson LS, Park S, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL

Genome Announc 2016 Sep 29. PMID: 27688327

Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis.

Robinson LS, Perry J, Lek S, Wollam A, Sodergren E, Weinstock G, Lewis WG, Lewis AL

Genome Announc 2016 Sep 29. PMID: 27688326

Antibiotic perturbation of the preterm infant gut microbiome and resistome.

Gasparrini AJ, Crofts TS, Gibson MK, Tarr PI, Warner BB, Dantas G

Gut Microbes 2016 Sep 2. PMID: 27472377

Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis.

Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV, Blaser MJ

J. Am. Acad. Dermatol. 2016 Sep . PMID: 27543211

Butyrate and bioactive proteolytic form of Wnt-5a regulate colonic epithelial proliferation and spatial development.

Uchiyama K, Sakiyama T, Hasebe T, Musch MW, Miyoshi H, Nakagawa Y, He TC, Lichtenstein L, Naito Y, Itoh Y, Yoshikawa T, Jabri B, Stappenbeck T, Chang EB

Sci Rep 2016 Aug 26. PMID: 27561676

The early infant gut microbiome varies in association with a maternal high-fat diet.

Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M, Aagaard KM

Genome Med 2016 Aug 09. PMID: 27503374

GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine.

Pokusaeva K, Johnson C, Luk B, Uribe G, Fu Y, Oezguen N, Matsunami RK, Lugo M, Major A, Mori-Akiyama Y, Hollister EB, Dann SM, Shi XZ, Engler DA, Savidge T, Versalovic J

Neurogastroenterol. Motil. 2016 Jul 25. PMID: 27458085

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

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

Nature 2016 Jul 21. PMID: 27409808

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

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

ISME J 2016 Jul . PMID: 26905627

Necrotizing enterocolitis and preterm infant gut bacteria.

Warner BB, Tarr PI

Semin Fetal Neonatal Med 2016 Jun 22. PMID: 27343151

Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study.

Warner BB, Deych E, Zhou Y, Hall-Moore C, Weinstock GM, Sodergren E, Shaikh N, Hoffmann JA, Linneman LA, Hamvas A, Khanna G, Rouggly-Nickless LC, Ndao IM, Shands BA, Escobedo M, Sullivan JE, Radmacher PG, Shannon WD, Tarr PI

Lancet 2016 May 7. PMID: 26969089

Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome.

Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ

PLoS ONE 2016 . PMID: 27088867

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype.

Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD

Nat Microbiol 2016 Apr 04. PMID: 27572644

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

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation.

Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD

MBio 2016 Mar 29. PMID: 27025251

Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome.

Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G

Nat Microbiol 2016 Mar 07. PMID: 27572443

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 Mar . PMID: 26747455

Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens.

Zhou Y, Wylie KM, El Feghaly RE, Mihindukulasuriya KA, Elward A, Haslam DB, Storch GA, Weinstock GM

J. Clin. Microbiol. 2016 Feb . PMID: 26637379

The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults.

Barnett C, Nazzal L, Goldfarb DS, Blaser MJ

J. Urol. 2016 Feb . PMID: 26292041

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

Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review.

Guma S, Maglantay R, Lau R, Wieczorek R, Melamed J, Deng FM, Zhou M, Makarov D, Lee P, Pincus MR, Pei ZH

Am J Clin Exp Urol 2016 . PMID: 27069958

Erratum to: 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 2016 Jan 21. PMID: 26796629

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

STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW.

Hoffmann D, Schwartz J

Am J Law Med 2016 . PMID: 27263263

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

Carcass mass has little influence on the structure of gravesoil microbial communities.

Weiss S, Carter DO, Metcalf JL, Knight R

Int. J. Legal Med. 2016 Jan . PMID: 26024793

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 Dec 15. PMID: 26670383

The microbiome quality control project: baseline study design and future directions.

Sinha R, Abnet CC, White O, Knight R, Huttenhower C

Genome Biol. 2015 Dec 09. PMID: 26653756

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 Dec 01. PMID: 26620712

Luminal Conversion and Immunoregulation by Probiotics.

Ganesh BP, Versalovic J

Front Pharmacol 2015 . PMID: 26617521

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

Global prevalence and distribution of genes and microorganisms involved in mercury methylation.

Podar M, Gilmour CC, Brandt CC, Soren A, Brown SD, Crable BR, Palumbo AV, Somenahally AC, Elias DA

Sci Adv 2015 Oct . PMID: 26601305

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 Sep 15. 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 Aug 26. 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

High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.

Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Durkin AS, Nelson KE, Epstein SS

Stand Genomic Sci 2015 . PMID: 26221418

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 Jun 30. PMID: 26123276

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

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 Jun 16. 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

The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome.

Davidovics ZH, Carter BA, Luna RA, Hollister EB, Shulman RJ, Versalovic J

JPEN J Parenter Enteral Nutr 2015 Jun 9. PMID: 26059898

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

Inflammation-associated microbiota in pediatric eosinophilic esophagitis.

Benitez AJ, Hoffmann C, Muir AB, Dods KK, Spergel JM, Bushman FD, Wang ML

Microbiome 2015 . PMID: 26034601

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

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

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

Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis.

Kellermayer R, Nagy-Szakal D, Harris RA, Luna RA, Pitashny M, Schady D, Mir SA, Lopez ME, Gilger MA, Belmont J, Hollister EB, Versalovic J

Am. J. Gastroenterol. 2015 Apr . PMID: 25853207

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 Mar 25. 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 Mar 17. PMID: 25343515

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

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

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

Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility.

Sankar PL, Cho MK

Am J Bioeth 2015 . PMID: 26632356

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

De novo large cell neuroendocrine carcinoma of the prostate, case report and literature review.

Acosta-Gonzalez G, Qin J, Wieczorek R, Melamed J, Deng FM, Zhou M, Makarov D, Ye F, Pei Z, Pincus MR, Lee P

Am J Clin Exp Urol 2014 . PMID: 25606580

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

Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution.

Wu M, Singh AK

J Lab Autom 2014 Dec . PMID: 25027027

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 Nov 19. PMID: 25407910

Meta-analyses of human gut microbes associated with obesity and IBD.

Walters WA, Xu Z, Knight R

FEBS Lett. 2014 Nov 17. PMID: 25307765

The conjunctival microbiome in health and trachomatous disease: a case control study.

Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM, Burr SE

Genome Med 2014 . PMID: 25484919

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 Nov 04. 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 Oct 23. PMID: 25344410

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

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 Sep 10. PMID: 25212266

The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.

Cell Host Microbe 2014 Sep 10. PMID: 25211071

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

Conducting a microbiome study.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE

Cell 2014 Jul 17. PMID: 25036628

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 Jul 08. 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 Jul 02. 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 Jun 27. PMID: 24995464

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R

Front Microbiol 2014 . PMID: 24995004

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 Jun 19. 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 Jun 17. PMID: 24939888

Versatile on-demand droplet generation for controlled encapsulation.

Rhee M, Liu P, Meagher RJ, Light YK, Singh AK

Biomicrofluidics 2014 May . PMID: 25379072

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 May 22. 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

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

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 May 07. PMID: 24887286

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

Diet and the intestinal microbiome: associations, functions, and implications for health and disease.

Albenberg LG, Wu GD

Gastroenterology 2014 May . PMID: 24503132

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

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

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

Vital M, Howe AC, Tiedje JM

MBio 2014 Apr 22. 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

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

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 16. 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

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

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

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 Feb 24. PMID: 24558975

Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35.

Boonma P, Spinler JK, Qin X, Jittaprasatsin C, Muzny DM, Doddapaneni H, Gibbs R, Petrosino J, Tumwasorn S, Versalovic J

Stand Genomic Sci 2014 Jun 15. PMID: 25197459

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. PMID: 24529162

Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia.

Beall CJ, Campbell AG, Dayeh DM, Griffen AL, Podar M, Leys EJ

PLoS ONE 2014 . PMID: 24551246

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

Segal LN, Blaser MJ

Ann Am Thorac Soc 2014 Jan . PMID: 24437400

Microbiome in reflux disorders and esophageal adenocarcinoma.

Yang L, Chaudhary N, Baghdadi J, Pei Z

Cancer J . PMID: 24855009

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

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

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

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

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 Dec 02. 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 Nov 27. PMID: 24279426

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

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

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 Nov 01. 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 Oct 14. PMID: 24124697

FunGene: the functional gene pipeline and repository.

Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, Cole JR

Front Microbiol 2013 . PMID: 24101916

Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.

Wang Q, Quensen JF, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR

MBio 2013 Sep 17. PMID: 24045641

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 Aug 22. 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 Aug 22. PMID: 23965294

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

Virome genomics: a tool for defining the human virome.

Wylie KM, Weinstock GM, Storch GA

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

Gene expression profiles in febrile children with defined viral and bacterial infection.

Hu X, Yu J, Crosby SD, Storch GA

Proc. Natl. Acad. Sci. U.S.A. 2013 Jul 30. PMID: 23858444

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

Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach.

Cleeland LM, Reichard MV, Tito RY, Reinhard KJ, Lewis CM

J. Archaeol. Sci. 2013 Jul 1. PMID: 23645967

Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project.

Hoffmann DE, Fortenberry JD, Ravel J

J Law Med Ethics 2013 . PMID: 23802897

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 Jun 06. 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

Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period.

Shkoporov AN, Efimov BA, Khokhlova EV, Chaplin AV, Kafarskaya LI, Durkin AS, McCorrison J, Torralba M, Gillis M, Sutton G, Weibel DB, Nelson KE, Smeianov VV

Genome Announc 2013 May 16. PMID: 23682142

Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.

Hettich RL, Pan C, Chourey K, Giannone RJ

Anal. Chem. 2013 May 7. PMID: 23469896

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

Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome.

Tomida S, Nguyen L, Chiu BH, Liu J, Sodergren E, Weinstock GM, Li H

MBio 2013 Apr 30. PMID: 23631911

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

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

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

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

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BMC Med Ethics 2012 Oct 30. PMID: 23110633

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

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