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JOSEPH PETROSINO

TitleInterim Chair
InstitutionBaylor College of Medicine
DepartmentDepartment of Molecular Virology & Microbiology
DivisionMolecular Virology & Microbiology
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    Other Positions
    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Molecular Virology & Microbiology
    DivisionMolecular Virology & Microbiology

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentDepartment of Ophthalmology
    DivisionOphthalmology

    TitleProfessor
    InstitutionBaylor College of Medicine
    DepartmentHuman Genome Sequencing Center
    DivisionHuman Genome Sequencing Center


    Collapse ORNG Applications 
    Collapse Verify Publications

    Collapse Biography 
    Collapse awards and honors
    2013 - 2014Honoree of Houston Men of Distinction, Houston Men of Distinction
    2012 - 2014ASM Distinguished Lecturer, American Society for Microbiology
    2005 - 2007Career Development Award, Western Regional Center of Excellence for Biodefense and Emerging Infectious Disease
    2000 - 2003Breast Cancer Initiative Postdoctoral Fellowship, United States Army Materiel Command
    2000Postdoctoral Fellowship (declined), American Cancer Society
    2000National Research Service Award Postdoctoral Fellowship (declined), National Institutes of Health
    1999Postdoctoral Genetics Training Grant Appointee, National Institutes of Health
    1997Honorable Mention, S.E. Sulkin Award for Clinical and Applied Microbiology, American Society for Microbiology-Texas Branch

    Collapse Overview 
    Collapse overview
    Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. The total number of genes in the human microbiome may exceed the total number of human genes by a factor of 100 to 1. These microbial communities comprise what has come to be known as the ‘human microbiome’. Until recently, the human microbiome has been largely unstudied, leaving its influence upon human health largely unknown. Traditional microbiology has focused on the study of individual isolated species, with most organisms (>80%) having never been successfully cultured. However, advances in DNA sequencing technologies have created the ability to examine microbial communities, including uncultivable organisms. These advances have led to ‘metagenomic’ approaches that allow the analysis of genetic material derived from complete microbial communities harvested from natural environments, thus facilitating the study of the human microbiome as well as the microbiomes of other animals and environmental niches.

    To take advantage of these recent technological advances, the NIH Roadmap Office/Common Fund initiated the Human Microbiome Project (HMP) in 2006 with the mission of generating resources enabling characterization of the human microbiota and analysis of its role in human health and disease. As a Primary Investigator in the HMP, and in directing a number of other microbiome projects, my interests are focused on developing and implementing measures to sample and analyze microbial communities from niches on and in the human body and related animal models for the understanding of how commensal organisms impact health and disease.

    Knowledge of how the microbiota impact and/or respond to various states of health and illness is vital for the development of treatments that can diagnose, treat and/or eliminate heritable or infectious disease. For example, microbiome-associated diagnostics may be more sensitive for detecting certain diseases and/or predicting susceptibility to others so that appropriate precautions can be made (e.g., taking a probiotic or antibiotic when traveling when it’s known that an individual is highly susceptible to travelers’ diarrhea or Norwalk virus infection).

    Since the onset of the HMP, we along with collaborators in the Department of Molecular Virology and Microbiology (MVM) and the Human Genome Sequencing Center have been pursuing diverse projects in metagenomics and microbiome research. In 2011 I established the Alkek Center for Metagenomics and Microbiome Research (CMMR) at BCM to maintain our position as leaders in this field, and to further develop and expand the infrastructure and expertise that will propel microbiome research in the future with the following mission foci:

    Support existing metagenomic research programs that are ongoing at BCM and affiliated institutions

    Provide support for investigators/clinical collaborators who have ideal model systems for metagenomics but who do not know where to begin such studies.

    Expand metagenomic research into animal and molecular model systems so that hypothesis-driven research could be initiated and supported.

    Provide a critical mass in bioinformatic expertise for analyzing and providing statistical support for metagenomic data.

    Translate novel discoveries from microbiome studies to effective clinical therapeutics and diagnostics.

    Among the largest of the more than 250 projects we are engaging/have engaged with over 120 collaborating groups from around the world during the past 4 years is a comprehensive microbiome analysis supporting the NIDDK-funded TEDDY (The Environmental Determinants of Diabetes in the Young) Project. The goal of this study is to identify microbial associations and triggers that may underlie the onset of type 1 diabetes. This knowledge will hopefully lead to better diagnostics, interventions, and perhaps even a cure, for juvenile diabetes.

    Other collaborations with researchers at BCM and other area institutions have led to a number of ongoing lucrative projects, some of which have been highlighted elsewhere in the BCM and national spotlight. We anticipate these studies will produce results that may translate directly into therapeutics and diagnostics that impact human health. Among these are projects with Drs. Danny Jones and Stephen Pflugfelder, Department of Ophthalmology, studying the ocular surface microbiome associated with health and disease, Dr. James Versalovic, Department of Pathology, TCH Microbiome Center, focusing on microbiome associations to pediatric bowel pain, Dr. Kjersti Aagaard, Department of Obstetrics and Gynecology, on microbiome associations to pre-term birth, Drs. Herbert DuPont and David Graham, Department of Medicine, examining microbiota associations with gastrointestinal disease and treatment with fecal transplants and defined microbial communities. Each of these projects has posed unique study design and technology challenges that CMMR staff and collaborators are addressing to generate provocative results that will hopefully benefit human health in the near future.

    ____________________________________________________________________

    Independent from our research on the human microbiome, we are also actively studying the biodefense concern, Francisella tularensis.

    The facultative intracellular pathogen, Francisella tularensis, is the causative agent of tularemia, and is among the most infectious pathogens known, both in terms of the number of zoonotic species it infects (>250), and the number of organisms needed to establish a potentially lethal infection (<10 by the airborne route). F. tularensis is a Category A biodefense agent because of its ability to cause incapacitating, potentially fatal, illness, its ability to spread via aerosolization, and for the potential burden it would have on the public health system in the event of an outbreak. There are four subspecies of Francisella tularensis: subspecies tularensis (Type A), subspecies holarctica (Type B), subspecies novicida, and subspecies mediasiatica. Type A, found exclusively in North America and Mexico, causes the most severe form of human disease, while Type B is less pathogenic in humans and is found throughout the northern hemisphere. Several decades ago, in the former Soviet Union, an attenuated live vaccine strain (LVS) was derived from repeated passage of a Type B strain. LVS offers protection against both Type A and Type B infection, but is not licensed for use in the U.S. because it’s immunogenicity in humans is poorly characterized, the mechanism of attenuation for this strain is unknown, and the strain kills mice with a LD50 of one bacterium when injected intraperitoneally.

    Using state-of-the-art technologies and resources in the Baylor College of Medicine Human Genome Sequencing Center, we are determining the genomic sequences of multiple F. tularensis strains. Comparisons of Type A, Type B, LVS, and other Francisella sequences are highlighting genetic differences that will answer the following questions:

    Why are Type A Francisella strains more virulent than Type B strains?

    How are Francisella subspecies evolutionarily related?

    What makes Francisella so pathogenic in the absence of an obvious toxin?

    What genes mediate robust replication of Francisella in macrophages?

    What mutations attenuate LVS?

    What mutations are capable of rationally attenuating pathogenic strains?

    Isogenic Francisella mutant strains will be constructed subsequently to test the roles of candidate alleles in strain attenuation and host specificity. These studies will reveal the pathogenicity mechanisms of one of the most virulent bacteria known and will further the development of improved attenuated vaccines and immunodiagnostics targeted against Francisella.

    Functional genomics approaches are being used to identify proteins important for F. tularensis recognition by the host immune response. With our collaborators, we are using the recombination-based, Gateway system (Invitrogen, Carlsbad, CA) to clone and express approximately 2000 open reading frames (ORFs) belonging to the Type A and Type B Francisella subspecies. This strategy permits the rapid conversion of the original plasmid clone set to other functional vectors containing various promoters or tag sequences. Through further collaboration with the BCM Vaccine Treatment and Evaluation Unit (VTEU) we are using this clone set, along with the shotgun library constructed to sequence the Francisella genome, to systematically identify F. tularensis proteins recognized by the human humoral and cell-mediated immune responses. Results from this work will further characterize the human response to LVS vaccination and will lead to the development of novel F. tularensis vaccines and immunodiagnostics.

    The approaches outlined here are being adapted for additional functional genomics studies in other biodefense and emerging and infectious disease concerns to advance vaccine and diagnostic discovery in these organisms.

    Collapse Research 
    Collapse research activities and funding
    U54HG004973     (GIBBS, RICHARD A)Jun 19, 2009 - Apr 30, 2013
    NIH/NHGRI
    A Microbial Genome Reference Platform for Metagenomics
    Role: Co-Principal Investigator

    R01DK109588     (GOODARZI, MARK)Apr 1, 2017 - Mar 31, 2022
    NIH/NIDDK
    Impact of the gut microbiome and diet on change in insulin homeostasis and cardiometabolic risk
    Role: Co-Principal Investigator

    R21ES029493     (PETROSINO, JOSEPH FRANK)Mar 1, 2018 - Feb 29, 2020
    NIH/NIEHS
    Incorporating the Microbiome into DR2 Activities to Inform Health Outcomes
    Role: Principal Investigator

    R56ES030221     (MOORTHY, BHAGAVATULA)Feb 1, 2019 - Jan 31, 2020
    NIH/NIEHS
    Prenatal exposure to PAHs and hyperoxic lung injury: Role of the microbiome
    Role: Co-Principal Investigator

    U19AI144297     (PETROSINO, JOSEPH FRANK)Apr 15, 2019 - Mar 31, 2024
    NIH/NIAID
    Integrated Genomics of Mucosal Infections
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, Scheet P, Xu H, Hanash SM, Feng L, Burks JK, Do KA, Peterson CB, Nejman D, Tzeng CD, Kim MP, Sears CL, Ajami N, Petrosino J, Wood LD, Maitra A, Straussman R, Katz M, White JR, Jenq R, Wargo J, McAllister F. Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Cell. 2019 Aug 08; 178(4):795-806.e12. PMID: 31398337.
      View in: PubMed
    2. Liu Y, Ajami NJ, El-Serag HB, Hair C, Graham DY, White DL, Chen L, Wang Z, Plew S, Kramer J, Cole R, Hernaez R, Hou J, Husain N, Jarbrink-Sehgal ME, Kanwal F, Ketwaroo G, Natarajan Y, Shah R, Velez M, Mallepally N, Petrosino JF, Jiao L. Dietary quality and the colonic mucosa-associated gut microbiome in humans. Am J Clin Nutr. 2019 Jul 10. PMID: 31291462.
      View in: PubMed
    3. Faucher MA, Greathouse KL, Hastings-Tolsma M, Padgett RN, Sakovich K, Choudhury A, Sheikh A, Ajami NJ, Petrosino JF. Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study. Am J Perinatol. 2019 Jun 26. PMID: 31242511.
      View in: PubMed
    4. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019 May; 569(7758):655-662. PMID: 31142855.
      View in: PubMed
    5. Stewart CJ, Mansbach JM, Ajami NJ, Petrosino JF, Zhu Z, Liang L, Camargo CA, Hasegawa K. Serum Metabolome Is Associated With the Nasopharyngeal Microbiota and Disease Severity Among Infants With Bronchiolitis. J Infect Dis. 2019 May 24; 219(12):2005-2014. PMID: 30629185.
      View in: PubMed
    6. Toivonen L, Hasegawa K, Waris M, Ajami NJ, Petrosino JF, Camargo CA, Peltola V. Early nasal microbiota and acute respiratory infections during the first years of life. Thorax. 2019 Jun; 74(6):592-599. PMID: 31076501.
      View in: PubMed
    7. Mansbach JM, Hasegawa K, Piedra PA, Avadhanula V, Petrosino JF, Sullivan AF, Espinola JA, Camargo CA. Haemophilus-Dominant Nasopharyngeal Microbiota Is Associated With Delayed Clearance of Respiratory Syncytial Virus in Infants Hospitalized for Bronchiolitis. J Infect Dis. 2019 May 05; 219(11):1804-1808. PMID: 30590603.
      View in: PubMed
    8. Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn. 2019 May; 21(3):449-461. PMID: 31005411.
      View in: PubMed
    9. Gurwara S, Ajami NJ, Jang A, Hessel FC, Chen L, Plew S, Wang Z, Graham DY, Hair C, White DL, Kramer J, Kourkoumpetis T, Hoffman K, Cole R, Hou J, Husain N, Jarbrink-Sehgal M, Hernaez R, Kanwal F, Ketwaroo G, Shah R, Velez M, Natarajan Y, El-Serag HB, Petrosino JF, Jiao L. Dietary Nutrients Involved in One-Carbon Metabolism and Colonic Mucosa-Associated Gut Microbiome in Individuals with an Endoscopically Normal Colon. Nutrients. 2019 Mar 13; 11(3). PMID: 30871224.
      View in: PubMed
    10. Stewart CJ, Fatemizadeh R, Parsons P, Lamb CA, Shady DA, Petrosino JF, Hair AB. Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue. BMC Microbiol. 2019 Mar 04; 19(1):52. PMID: 30832576.
      View in: PubMed
    11. Tribble GD, Angelov N, Weltman R, Wang BY, Eswaran SV, Gay IC, Parthasarathy K, Dao DV, Richardson KN, Ismail NM, Sharina IG, Hyde ER, Ajami NJ, Petrosino JF, Bryan NS. Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. Front Cell Infect Microbiol. 2019; 9:39. PMID: 30881924.
      View in: PubMed
    12. Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J, Petrosino JF, Kellermayer R. Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model. Gut Microbes. 2019; 10(4):504-520. PMID: 30663928.
      View in: PubMed
    13. Curtis K, Stewart CJ, Robinson M, Molfese DL, Gosnell SN, Kosten TR, Petrosino JF, De La Garza R, Salas R. Insular resting state functional connectivity is associated with gut microbiota diversity. Eur J Neurosci. 2018 Dec 16. PMID: 30554441.
      View in: PubMed
    14. Ramani S, Stewart CJ, Laucirica DR, Ajami NJ, Robertson B, Autran CA, Shinge D, Rani S, Anandan S, Hu L, Ferreon JC, Kuruvilla KA, Petrosino JF, Venkataram Prasad BV, Bode L, Kang G, Estes MK. Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection. Nat Commun. 2018 11 27; 9(1):5010. PMID: 30479342.
      View in: PubMed
    15. Toivonen L, Hasegawa K, Ajami NJ, Celedón JC, Mansbach JM, Petrosino JF, Camargo CA. Circulating 25-hydroxyvitamin D, nasopharyngeal microbiota, and bronchiolitis severity. Pediatr Allergy Immunol. 2018 12; 29(8):877-880. PMID: 30152883.
      View in: PubMed
    16. Jiang ZD, Jenq RR, Ajami NJ, Petrosino JF, Alexander AA, Ke S, Iqbal T, DuPont AW, Muldrew K, Shi Y, Peterson C, Do KA, DuPont HL. Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial. PLoS One. 2018; 13(11):e0205064. PMID: 30388112.
      View in: PubMed
    17. Ganesh BP, Nelson JW, Eskew JR, Ganesan A, Ajami NJ, Petrosino JF, Bryan RM, Durgan DJ. Prebiotics, Probiotics, and Acetate Supplementation Prevent Hypertension in a Model of Obstructive Sleep Apnea. Hypertension. 2018 11; 72(5):1141-1150. PMID: 30354816.
      View in: PubMed
    18. Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018 10; 562(7728):583-588. PMID: 30356187.
      View in: PubMed
    19. Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ. The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018 10; 562(7728):589-594. PMID: 30356183.
      View in: PubMed
    20. Liu Y, O'Brien JL, Ajami NJ, Scheurer ME, Amirian ES, Armstrong G, Tsavachidis S, Thrift AP, Jiao L, Wong MC, Smith DP, Spitz MR, Bondy ML, Petrosino JF, Kheradmand F. Lung tissue microbial profile in lung cancer is distinct from emphysema. Am J Cancer Res. 2018; 8(9):1775-1787. PMID: 30323970.
      View in: PubMed
    21. Stewart CJ, Auchtung TA, Ajami NJ, Velasquez K, Smith DP, De La Garza R, Salas R, Petrosino JF. Correction: Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study. PeerJ. 2018; 6. PMID: 30148001.
      View in: PubMed
    22. Ajami NJ, Wong MC, Ross MC, Lloyd RE, Petrosino JF. Maximal viral information recovery from sequence data using VirMAP. Nat Commun. 2018 08 10; 9(1):3205. PMID: 30097567.
      View in: PubMed
    23. Call L, Stoll B, Oosterloo B, Ajami N, Sheikh F, Wittke A, Waworuntu R, Berg B, Petrosino J, Olutoye O, Burrin D. Metabolomic signatures distinguish the impact of formula carbohydrates on disease outcome in a preterm piglet model of NEC. Microbiome. 2018 06 19; 6(1):111. PMID: 29921329.
      View in: PubMed
    24. Stewart CJ, Auchtung TA, Ajami NJ, Velasquez K, Smith DP, De La Garza R, Salas R, Petrosino JF. Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study. PeerJ. 2018; 6:e4693. PMID: 29736335.
      View in: PubMed
    25. Hoffman KL, Hutchinson DS, Fowler J, Smith DP, Ajami NJ, Zhao H, Scheet P, Chow WH, Petrosino JF, Daniel CR. Oral microbiota reveals signs of acculturation in Mexican American women. PLoS One. 2018; 13(4):e0194100. PMID: 29694348.
      View in: PubMed
    26. Houghton D, Stewart CJ, Stamp C, Nelson A, Aj Ami NJ, Petrosino JF, Wipat A, Trenell MI, Turnbull DM, Greaves LC. Impact of Age-Related Mitochondrial Dysfunction and Exercise on Intestinal Microbiota Composition. J Gerontol A Biol Sci Med Sci. 2018 04 17; 73(5):571-578. PMID: 29045670.
      View in: PubMed
    27. Kaur K, Saxena A, Debnath I, O'Brien JL, Ajami NJ, Auchtung TA, Petrosino JF, Sougiannis AJ, Depaep S, Chumanevich A, Gummadidala PM, Omebeyinje MH, Banerjee S, Chatzistamou I, Chakraborty P, Fayad R, Berger FG, Carson JA, Chanda A. Antibiotic-mediated bacteriome depletion in ApcMin/+ mice is associated with reduction in mucus-producing goblet cells and increased colorectal cancer progression. Cancer Med. 2018 05; 7(5):2003-2012. PMID: 29624892.
      View in: PubMed
    28. Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, Auchtung JM, Ajami NJ, Petrosino JF. Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere. 2018 Mar-Apr; 3(2). PMID: 29600282.
      View in: PubMed
    29. San-Juan-Vergara H, Zurek E, Ajami NJ, Mogollon C, Peña M, Portnoy I, Vélez JI, Cadena-Cruz C, Diaz-Olmos Y, Hurtado-Gómez L, Sanchez-Sit S, Hernández D, Urruchurtu I, Di-Ruggiero P, Guardo-García E, Torres N, Vidal-Orjuela O, Viasus D, Petrosino JF, Cervantes-Acosta G. A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South America. Sci Rep. 2018 Mar 14; 8(1):4479. PMID: 29540734.
      View in: PubMed
    30. Stewart CJ, Hasegawa K, Wong MC, Ajami NJ, Petrosino JF, Piedra PA, Espinola JA, Tierney CN, Camargo CA, Mansbach JM. Respiratory Syncytial Virus and Rhinovirus Bronchiolitis Are Associated With Distinct Metabolic Pathways. J Infect Dis. 2018 03 13; 217(7):1160-1169. PMID: 29293990.
      View in: PubMed
    31. Penington JS, Penno MAS, Ngui KM, Ajami NJ, Roth-Schulze AJ, Wilcox SA, Bandala-Sanchez E, Wentworth JM, Barry SC, Brown CY, Couper JJ, Petrosino JF, Papenfuss AT, Harrison LC. Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis. Sci Rep. 2018 Mar 12; 8(1):4386. PMID: 29531234.
      View in: PubMed
    32. Petrosino JF. The microbiome in precision medicine: the way forward. Genome Med. 2018 02 22; 10(1):12. PMID: 29471863.
      View in: PubMed
    33. Mulukutla SN, Hsu JW, Gaba R, Bohren KM, Guthikonda A, Iyer D, Ajami NJ, Petrosino JF, Hampe CS, Ram N, Jahoor F, Balasubramanyam A. Arginine Metabolism Is Altered in Adults with A-ß + Ketosis-Prone Diabetes. J Nutr. 2018 02 01; 148(2):185-193. PMID: 29490093.
      View in: PubMed
    34. Luna PN, Hasegawa K, Ajami NJ, Espinola JA, Henke DM, Petrosino JF, Piedra PA, Sullivan AF, Camargo CA, Shaw CA, Mansbach JM. The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Microbiome. 2018 01 03; 6(1):2. PMID: 29298732.
      View in: PubMed
    35. Nash AK, Auchtung TA, Wong MC, Smith DP, Gesell JR, Ross MC, Stewart CJ, Metcalf GA, Muzny DM, Gibbs RA, Ajami NJ, Petrosino JF. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome. 2017 Nov 25; 5(1):153. PMID: 29178920.
      View in: PubMed
    36. Hasegawa K, Linnemann RW, Mansbach JM, Ajami NJ, Espinola JA, Petrosino JF, Piedra PA, Stevenson MD, Sullivan AF, Thompson AD, Camargo CA. Nasal Airway Microbiota Profile and Severe Bronchiolitis in Infants: A Case-control Study. Pediatr Infect Dis J. 2017 Nov; 36(11):1044-1051. PMID: 28005692.
      View in: PubMed
    37. Robinson A, Fiechtner L, Roche B, Ajami NJ, Petrosino JF, Camargo CA, Taveras EM, Hasegawa K. Association of Maternal Gestational Weight Gain With the Infant Fecal Microbiota. J Pediatr Gastroenterol Nutr. 2017 11; 65(5):509-515. PMID: 28272161.
      View in: PubMed
    38. Stewart CJ, Mansbach JM, Wong MC, Ajami NJ, Petrosino JF, Camargo CA, Hasegawa K. Associations of Nasopharyngeal Metabolome and Microbiome with Severity among Infants with Bronchiolitis. A Multiomic Analysis. Am J Respir Crit Care Med. 2017 10 01; 196(7):882-891. PMID: 28530140.
      View in: PubMed
    39. Mansbach JM, Hasegawa K, Ajami NJ, Petrosino JF, Piedra PA, Tierney CN, Espinola JA, Camargo CA. Serum LL-37 Levels Associated With Severity of Bronchiolitis and Viral Etiology. Clin Infect Dis. 2017 Sep 15; 65(6):967-975. PMID: 28541502.
      View in: PubMed
    40. Gummadidala PM, Holder ME, O'Brien JL, Ajami NJ, Petrosino JF, Mitra C, Chen YP, Decho AW, Chanda A. Complete Genome Sequence of Vibrio gazogenes ATCC 43942. Genome Announc. 2017 Jul 27; 5(30). PMID: 28751405.
      View in: PubMed
    41. Hasegawa K, Stewart CJ, Mansbach JM, Linnemann RW, Ajami NJ, Petrosino JF, Camargo CA. Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case-control study. BMC Res Notes. 2017 Jul 26; 10(1):325. PMID: 28747215.
      View in: PubMed
    42. Lai PS, Allen JG, Hutchinson DS, Ajami NJ, Petrosino JF, Winters T, Hug C, Wartenberg GR, Vallarino J, Christiani DC. Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study. PLoS One. 2017; 12(7):e0180969. PMID: 28704437.
      View in: PubMed
    43. Stewart CJ, Embleton ND, Marrs ECL, Smith DP, Fofanova T, Nelson A, Skeath T, Perry JD, Petrosino JF, Berrington JE, Cummings SP. Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome. 2017 07 12; 5(1):75. PMID: 28701177.
      View in: PubMed
    44. Abrahamson M, Hooker E, Ajami NJ, Petrosino JF, Orwoll ES. Successful collection of stool samples for microbiome analyses from a large community-based population of elderly men. Contemp Clin Trials Commun. 2017 Sep; 7:158-162. PMID: 29250605.
      View in: PubMed
    45. Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol. 2017; 8:1008. PMID: 28634475.
      View in: PubMed
    46. Jacob V, Crawford C, Cohen-Mekelburg S, Viladomiu M, Putzel GG, Schneider Y, Chabouni F, O'Neil S, Bosworth B, Woo V, Ajami NJ, Petrosino JF, Gerardin Y, Kassam Z, Smith M, Iliev ID, Sonnenberg GF, Artis D, Scherl E, Longman RS. Single Delivery of High-Diversity Fecal Microbiota Preparation by Colonoscopy Is Safe and Effective in Increasing Microbial Diversity in Active Ulcerative Colitis. Inflamm Bowel Dis. 2017 06; 23(6):903-911. PMID: 28445246.
      View in: PubMed
    47. Carlson JM, Leonard AB, Hyde ER, Petrosino JF, Primm TP. Microbiome disruption and recovery in the fish Gambusia affinis following exposure to broad-spectrum antibiotic. Infect Drug Resist. 2017; 10:143-154. PMID: 28533691.
      View in: PubMed
    48. Ye X, Wang R, Bhattacharya R, Boulbes DR, Fan F, Xia L, Adoni H, Ajami NJ, Wong MC, Smith DP, Petrosino JF, Venable S, Qiao W, Baladandayuthapani V, Maru D, Ellis LM. Fusobacterium Nucleatum Subspecies Animalis Influences Proinflammatory Cytokine Expression and Monocyte Activation in Human Colorectal Tumors. Cancer Prev Res (Phila). 2017 Jul; 10(7):398-409. PMID: 28483840.
      View in: PubMed
    49. Pammi M, O'Brien JL, Ajami NJ, Wong MC, Versalovic J, Petrosino JF. Development of the cutaneous microbiome in the preterm infant: A prospective longitudinal study. PLoS One. 2017; 12(4):e0176669. PMID: 28448623.
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    52. Viladomiu M, Kivolowitz C, Abdulhamid A, Dogan B, Victorio D, Castellanos JG, Woo V, Teng F, Tran NL, Sczesnak A, Chai C, Kim M, Diehl GE, Ajami NJ, Petrosino JF, Zhou XK, Schwartzman S, Mandl LA, Abramowitz M, Jacob V, Bosworth B, Steinlauf A, Scherl EJ, Wu HJ, Simpson KW, Longman RS. IgA-coated E. coli enriched in Crohn's disease spondyloarthritis promote TH17-dependent inflammation. Sci Transl Med. 2017 02 08; 9(376). PMID: 28179509.
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    63. Shakhsheer BA, Versten LA, Luo JN, Defazio JR, Klabbers R, Christley S, Zaborin A, Guyton KL, Krezalek M, Smith DP, Ajami NJ, Petrosino JF, Fleming ID, Belogortseva N, Zaborina O, Alverdy JC. Morphine Promotes Colonization of Anastomotic Tissues with Collagenase - Producing Enterococcus faecalis and Causes Leak. J Gastrointest Surg. 2016 10; 20(10):1744-51. PMID: 27530446.
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    64. Kelly TN, Bazzano LA, Ajami NJ, He H, Zhao J, Petrosino JF, Correa A, He J. Gut Microbiome Associates With Lifetime Cardiovascular Disease Risk Profile Among Bogalusa Heart Study Participants. Circ Res. 2016 Sep 30; 119(8):956-64. PMID: 27507222.
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    67. Hasegawa K, Linnemann RW, Mansbach JM, Ajami NJ, Espinola JA, Petrosino JF, Piedra PA, Stevenson MD, Sullivan AF, Thompson AD, Camargo CA. The Fecal Microbiota Profile and Bronchiolitis in Infants. Pediatrics. 2016 07; 138(1). PMID: 27354456.
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    68. Buffington SA, Di Prisco GV, Auchtung TA, Ajami NJ, Petrosino JF, Costa-Mattioli M. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring. Cell. 2016 Jun 16; 165(7):1762-1775. PMID: 27315483.
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    70. de Paiva CS, Jones DB, Stern ME, Bian F, Moore QL, Corbiere S, Streckfus CF, Hutchinson DS, Ajami NJ, Petrosino JF, Pflugfelder SC. Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome. Sci Rep. 2016 Apr 18; 6:23561. PMID: 27087247.
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    71. Petrosyan V, Holder M, Ajami NJ, Petrosino JF, Sahasrabhojane P, Thompson EJ, Kalia A, Shelburne SA. Complete Genome Sequence of Streptococcus mitis Strain SVGS_061 Isolated from a Neutropenic Patient with Viridans Group Streptococcal Shock Syndrome. Genome Announc. 2016 Apr 07; 4(2). PMID: 27056234.
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    74. Kirpich IA, Petrosino J, Ajami N, Feng W, Wang Y, Liu Y, Beier JI, Barve SS, Yin X, Wei X, Zhang X, McClain CJ. Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease. Am J Pathol. 2016 Apr; 186(4):765-76. PMID: 27012191.
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    77. 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. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016 Jan 08; 351(6269):158-62. PMID: 26657285.
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    90. Massey VL, Stocke KS, Schmidt RH, Tan M, Ajami N, Neal RE, Petrosino JF, Barve S, Arteel GE. Oligofructose protects against arsenic-induced liver injury in a model of environment/obesity interaction. Toxicol Appl Pharmacol. 2015 May 01; 284(3):304-14. PMID: 25759243.
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    128. 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. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011 Nov; 141(5):1782-91. PMID: 21741921.
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    129. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol. 2011 May; 29(5):415-20. PMID: 21552244.
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    130. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011 Mar; 21(3):494-504. PMID: 21212162.
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    131. Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D. A catalog of reference genomes from the human microbiome. Science. 2010 May 21; 328(5981):994-9. PMID: 20489017.
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    132. Petrosino JF, Galhardo RS, Morales LD, Rosenberg SM. Stress-induced beta-lactam antibiotic resistance mutation and sequences of stationary-phase mutations in the Escherichia coli chromosome. J Bacteriol. 2009 Oct; 191(19):5881-9. PMID: 19648247.
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    133. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin Chem. 2009 May; 55(5):856-66. PMID: 19264858.
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    134. Gao H, Pattison D, Yan T, Klingeman DM, Wang X, Petrosino J, Hemphill L, Wan X, Leaphart AB, Weinstock GM, Palzkill T, Zhou J. Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display. PLoS One. 2008 Aug 20; 3(8):e2983. PMID: 18714347.
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    135. Matejková P, Strouhal M, Smajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, Molla MN, Albert TJ, Weinstock GM. Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol. 2008 May 15; 8:76. PMID: 18482458.
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    136. Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörgo B, Pósfai G, Weinstock GM, Blattner FR. The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol. 2008 Apr; 190(7):2597-606. PMID: 18245285.
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    137. Highlander SK, Hultén KG, Qin X, Jiang H, Yerrapragada S, Mason EO, Shang Y, Williams TM, Fortunov RM, Liu Y, Igboeli O, Petrosino J, Tirumalai M, Uzman A, Fox GE, Cardenas AM, Muzny DM, Hemphill L, Ding Y, Dugan S, Blyth PR, Buhay CJ, Dinh HH, Hawes AC, Holder M, Kovar CL, Lee SL, Liu W, Nazareth LV, Wang Q, Zhou J, Kaplan SL, Weinstock GM. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007 Nov 06; 7:99. PMID: 17986343.
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    138. Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Eswara Moorthy P, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One. 2007 Sep 26; 2(9):e928. PMID: 17895969.
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    139. Karpathy SE, Qin X, Gioia J, Jiang H, Liu Y, Petrosino JF, Yerrapragada S, Fox GE, Haake SK, Weinstock GM, Highlander SK. Genome sequence of Fusobacterium nucleatum subspecies polymorphum - a genetically tractable fusobacterium. PLoS One. 2007 Aug 01; 2(7):e659. PMID: 17668047.
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    140. Titball RW, Petrosino JF. Francisella tularensis genomics and proteomics. Ann N Y Acad Sci. 2007 Jun; 1105:98-121. PMID: 17435122.
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    141. Petrosino JF, Xiang Q, Karpathy SE, Jiang H, Yerrapragada S, Liu Y, Gioia J, Hemphill L, Gonzalez A, Raghavan TM, Uzman A, Fox GE, Highlander S, Reichard M, Morton RJ, Clinkenbeard KD, Weinstock GM. Chromosome rearrangement and diversification of Francisella tularensis revealed by the type B (OSU18) genome sequence. J Bacteriol. 2006 Oct; 188(19):6977-85. PMID: 16980500.
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    142. Hastings PJ, Slack A, Petrosino JF, Rosenberg SM. Adaptive amplification and point mutation are independent mechanisms: evidence for various stress-inducible mutation mechanisms. PLoS Biol. 2004 Dec; 2(12):e399. PMID: 15550983.
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    143. McCool JD, Long E, Petrosino JF, Sandler HA, Rosenberg SM, Sandler SJ. Measurement of SOS expression in individual Escherichia coli K-12 cells using fluorescence microscopy. Mol Microbiol. 2004 Sep; 53(5):1343-57. PMID: 15387814.
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    144. Petrosino JF, Pendleton AR, Weiner JH, Rosenberg SM. Chromosomal system for studying AmpC-mediated beta-lactam resistance mutation in Escherichia coli. Antimicrob Agents Chemother. 2002 May; 46(5):1535-9. PMID: 11959593.
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