OUR PUBLICATIONS ON HUMAN MICROBIOME

PEER REVIEWED ARTICLES

(*) corresponding author

2022

  1. Batista L, Robles V, Manichanh C, Ruiz L, Guagnozzi D, Pinsach F, Guarner F, Fernández-Bañares F.
    Colonic bacterial diversity and dysbiosis in active microscopic colitis as compared to chronic diarrhoea and healthy controls: effect of polyethylene glycol after bowel lavage for colonoscopy
    In Press

  2. Xie Z, Manichanh C*.
    FunOMIC: Pipeline with built-in Fungal Taxonomic and Functional Databases for Human Mycobiome Profiling
    bioRxiv

  3. Oyarzun I, Le Nevé B, Yañez F, Xie Z, Pichaud M, Serrano-Gómez G, Roca J, Veiga P, Azpiroz F, Tap J, Manichanh C*.
    Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet.
    Computational and Structural Biotechnology Journal, in press. Quartile 1.

2021

  1. Serrano-Gómez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, Machiels K, Guarner F, Vermeire S, Manichanh C*.
    Dysbiosis and relapse-related microbiome in inflammatory bowel disease: a shotgun metagenomic approach.
    Computational and Structural Biotechnology Journal. PMID: 34938418. Quartile 1.

  2. Yáñez F, Soler Z, Oliero M, Xie Z, Oyarzun I, Serrano-Gómez G, Manichanh C*.
    Integrating Dietary Data into Microbiome Studies: A Step Forward for Nutri-Metaomics.
    Nutrients. 2021 Aug 27;13(9):2978. doi: 10.3390/nu13092978. PMID: 34578856 . Quartile 1.

  3. Sarrabayrouse G, Elias A, Yáñez F, Mayorga L, Varela E, Bartoli C, Casellas F, Borruel N, Herrera de Guise C, Machiels K, Vermeire S, Manichanh C*.
    Fungal and Bacterial Loads: Noninvasive Inflammatory Bowel Disease Biomarkers for the Clinical Setting.
    mSystems. 2021 Mar 23;6(2):e01277-20. doi:10.1128/mSystems.01277-20. PMID: 33758031. Quartile 1.

  4. Vork L*, Penders J, Jalanka J, Bojic S, Van Kuijk SM, Salonen A, De Vos WM, Rajilić‐Stojanović M, Weerts ZZ, Masclee AA, Pozuelo M, Manichanh C*, Jonkers DM.
    Does day-to-day variability in stool consistency link to the fecal microbiota composition?
    Frontiers in Cellular and Infection Microbiology. PMID: 34458156. Quartile 1.

2020

  1. C d’Enfert, AK Kaune, LR Alaban, S Chakraborty, N Cole, M Delavy, D Kosmala, B Marsaux, R Fróis-Martins, M Morelli, D Rosati, M Valentine, Z Xie, Y Emritloll, P A Warn, F Bequet, ME Bougnoux, S Bornes, MS. Gresnigt, B Hube, ID. Jacobson, M Legrand, S Leibundgut-Landmann, C Manichanh, CA Munro, M G. Netea, K Queiroz, K Roget, V Thomas, C Thoral, P Van den Abbeele, A W. Walker and A J.P. Brown.
    The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives.
    FEMS Microbiology Reviews. PMID: 33232448. Decile 1.

  2. Machiels K, Pozuelo M, Martinez-De la Torre A, Xie Z, Pascal V, Sabino J, Santiago A, Campos D, Wolthuis A, D'Hoore A, De Hertogh, Ferrante M, Manichanh C*, Vermeire S*.
    Early postoperative endoscopic recurrence in Crohn’s disease is characterized by distinct microbiota recolonization.
    Journal of Crohn and Colitis. doi: 10.1093/ecco-jcc/jjaa081. PMID: 32333762. Quartile 1.

  3. Moretó M, Miró L, Amat C, Polo J, Manichanh C, Pérez-Bosque A.
    Dietary supplementation with spray-dried porcine plasma has prebiotic effects on gut microbiota in mice.
    Sci Rep. doi: 10.1038/s41598-020-59756-z. PMID: 32076042. Quartile 1.

  4. Le Nevé B, de la Torre AM, Tap J, Derrien M, Cotillard A, Barba E, Mego M,Nieto Ruiz A, Hernandez-Palet L, Dornic Q, Faurie JM, Butler J, Merino X, Lobo B, Batet FP, Accarino A, Pozuelo M, Manichanh C, Azpiroz F.
    A Fermented Milk Product with B. Lactis CNCM I-2494 and Lactic Acid Bacteria Improves Gastrointestinal Comfort in Response to a Challenge Diet Rich in Fermentable Residues in Healthy Subjects.
    Nutrients. doi: 10.3390/nu12020320; PMID: 31991794. Quartile 1.

  5. Sarrabayrouse G, Landolfi S, Pozuelo M, Willamil J, Varela E, Clark A, Campos D, Herrera C, Santiago A, Machiels K, Vermeire S, Martí M, Espin E, Manichanh C*.
    Mucosal microbial load in Crohn's disease: A potential predictor of response to faecal microbiota transplantation.
    EBioMedicine - The Lancet, PMID: 31901867. Decile 1

2019

  1. Lleal M, Sarrabayrouse G, Willamil J, Santiago A, Pozuelo M, Manichanh C*.
    A single faecal microbiota transplantation modulates the microbiome and improves clinical manifestations in a rat model of colitis.
    EBioMedicine - The Lancet. PMID: 31628021. Decile 1

  2. Román E, Nieto JC, Gely C, Vidal S, Pozuelo M, Poca M, Juárez C, Guarner C, Manichanh C, and Soriano G.
    Effect of a Multistrain Probiotic on Cognitive Function and Risk of Falls in Patients With Cirrhosis: A Randomized Trial.
    Hepatology Communications. doi: 10.1002/hep4.1325.

  3. Santiago A, Sanchez E, Clark A, Pozuelo M, Calvo M, Yañez F, Sarrabayrouse G, Perea L, Vidal S, Gallardo A, Guarner C, Soriano G*, Chaysavanh Manichanh C*.
    Sequential changes in the mesenteric lymph node microbiome and immune response during cirrhosis induction in rats.
    mSystems. PMID: 30801032. Quartile 1

2018

  1. Hanachi M; Manichanh C*; Schoenenberger A; Pascal V; Levenez F; Cournede N; Doré J; Melchior JC.
    Altered host-gut microbes symbiosis in severely malnourished anorexia nervosa (AN) patients undergoing enteral nutrition: an explicative factor of functional intestinal disorders?
    Clinical Nutrition (PMID: 30527539). Decile 1.

  2. Huaman JW, Mego M, Manichanh C, Cañellas N, Cañueto D, Segurola H, Jansana M, Malagelada C, Accarino A, Vulevic J, Tzortzis G, Gibson G, Saperas E, Guarner F, Azpiroz F.
    Effects of Prebiotics vs a Diet Low in Fodmaps in Patients with Functional Gut Disorder.
    Gastroenterology (PMID: 29964041). Decile 1.

  3. Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, Clavel T, Panda S, Ludwig C, Kuster B, Manichanh C, Kump P, Haller D, Hörmannsperger G.
    Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis.
    Cell Mol Gastroenterol Hepatol. (PMID: 30182050).

2017

  1. García-Lezana T, Raurell I, Bravo M, Torres-Arauz M, Teresa Salcedo M, Alba S, Schoenenberger A, Manichanh C, Genescà J, Martell M, Augustin S.
    Restoration of a Healthy Intestinal Microbiota by Faecal Transplantation Normalizes Portal Hypertension and Endothelial Dysfunction in a Rat Model of Diet-Induced Nonalcoholic Steatohepatitis.
    Hepatology (PMID: 29113028). Decile 1.

  2. Gómez-Hurtado I, Giménez P, Garcia-Martinez I, Zapater P, Francés R, González-Navajas J, Manichanh C, Ramos JM, Bellot P, Guarner F, Such J.
    Norfloxacin is more effective than Rifaximin in avoiding bacterial translocation in an animal model of cirrhosis.
    Liver International (PMID: 28834270). Quartile 1.

  3. Costea et al. (IHMS consortium, including Manichanh C)
    Towards standards for human fecal sample processing in metagenomic studies.
    Nature Biotechnology (PMID: 28967887). Decile 1

  4. Sanchez E, Nieto J, Vidal S, Santiago A, Martinez X, Sancho FJ, Sancho-Bru P, Mirelis B, Corominola H, Juarez C, Manichanh C, Guarner C, Soriano G.
    Fermented milk containing Lactobacillus paracasei subsp. paracasei CNCM I-1518 reduces bacterial translocation in rats treated with carbon tetrachloride.
    Scientific Reports (PMID: 28368023). Quartile 1.

  5. Faner R, Sibila O, Agustí A, Bernasconi E, Chalmers JD, Huffnangle GB, Manichanh C, Molyneaux P, Paredes R, Brocal VP, Ponomarenko J, Sethi S, Dorca J, Monsó E.
    The Microbiome in Respiratory Medicine: Current Challenges and Future Perspectives.
    European Respiratory Journal (PMID: 28404649). Decile 1.

  6. Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, Martinez X, Varela E, Sarrabayrouse G, Machiels K, Vermeire S, Sokol H, Guarner F and Manichanh C*.
    A Microbial Signature for Crohn’s Disease.
    Gut (PMID: 28179361). A microbial signature for Crohn's disease Decile 1.

  7. Mego M, Manichanh C, Accarino A, Campos D, Pozuelo M, Varela E, Vulevic J, Tzortzis G, Gibson G, Guarner F, Azpiroz F.
    Metabolic Adaptation of Colonic Microbiota to Diet.
    Alimentary Pharmacology & Therapeutics (PMID: 28078750). Quartile 1.

2016

  1. Azpiroz F, Molne L, Mendez S, Nieto A, Manichanh C, Mego M, Accarino A, Santos J, Sailer M, Theis S, Guarner F.
    Effect of Chicory-derived Inulin on Abdominal Sensations and Bowel Motor Function.
    J Clin Gastroenterol. (PMID: 27680592)

  2. Plichta D, Juncker A, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Dantas Machado A, Evgrafov M, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O, Sommer M, Ehrlich D, Sicheritz-Pontén T, Brunak S, Nielsen HB.
    Transcriptional interactions suggest niche segregation among microbes in the human gut.
    Nature Microbiology (PMID: 27564131).

  3. Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O.
    Human gut microbes impact host serum metabolome and insulin sensitivity.
    Nature (PMID: 27409811). Decile 1.

  4. Martinez X, Pozuelo M, Pascal V, Campos D, Gut I, Gut M, Azpiroz F, Guarner F, Manichanh C*.
    MetaTrans: an open-source pipeline for metatranscriptomics.
    Scientific Reports (PMID: 27211518). Quartile 1.

  5. Santiago A, Pozuelo M, Poca M, Gely C, Nieto JC, Torras X, Román E, Campos D, Sarrabayrouse G, Vidal S, Guarner F, Soriano G, Manichanh C*, Guarner C.
    Alteration of the serum microbiome composition in cirrhotic patients with ascites.
    Scientific Reports (PMID: 27112233). Quartile 1.

2015

  1. Forslund F et al. (METAHIT Consortium)
    Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
    Nature (PMID: 26633628 ). Decile 1

  2. Marta Pozuelo#, Suchita Panda#, Alba Santiago, Sara Mendez, Anna Accarino, Javier Santos, Francisco Guarner, Fernando Azpiroz and Chaysavanh Manichanh* (#same contribution).
    Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome.
    Scientific Reports (PMID: 26239401). Quartile 1

  3. Rajilić-Stojanović M, Jonkers DM. , Salonen A, Hanevik K, Raes J, Jalanka J, de Vos WM, Manichanh C, Golic N, Enck P, Philippou E, Iraqi FA, Clarke G, Spiller RC, and Penders J.
    Intestinal microbiota and diet in IBS: causes, consequences or epiphenomena.
    American J Gastro. (PMID: 25623659). Decile 1

2014

  1. Panda S, Guarner F, Manichanh C*.
    Structure And Functions Of The Gut Microbiome.
    Endocr Metab Immune Disord Drug Targets (PMID: 25022563)

  2. Li J et al (Including Manichanh C).
    An integrated catalog of reference genes in the human gut micro biome.
    Nature Biotechnology (PMID: 24997786). Decile 1

  3. Santiago A, Panda S, Mengels G, Martínez X, Azpiroz F, Dore J, Guarner F, Manichanh C*.
    Processing faecal samples: a step forward for standards in microbial community analysis
    BMC Microbiology (PMID: 24884524). Quartile 2

  4. Nielsen HB, et al (including Manichanh C).
    Dependencies among metagenomic species, viruses, plasmids and units of genetic variation.
    Nature Biotechnology (PMID: 24997787). Decile 1

  5. Panda S, El khader I, Casellas F, López Vivancos J, García Cors M, Cuenca S, Guarner F and Manichanh C*
    Unexpected effect of antibiotics on human gut microbiota
    Plos One (PMID: 24748167). Quartile 1

  6. Cuenca S, Sanchez E, Santiago A, El khader I, Panda S, Vidal S, Camilo Nieto J, Juárez C, Sancho F, Guarner FC, Soriano G, Guarner C, Manichanh C*
    Microbial dysbiosis in the mesenteric lymph nodes of CCl4-induced cirrhotic rats
    Journal Innate Immunity, 6(3):263-71. Quartile 1

  7. Martínez-García B, Fernández X, Díaz-Ingelmo O, Rodríguez-Campos A, Manichanh C and Roca J
    Topoisomerase II minimizes DNA entanglements by proofreading DNA topology after DNA strand passage
    Nucleic Acids Res. 2014 Feb;42(3):1821-30. Decile 1

  8. Manichanh C, Eck A, Varela E, Roca J, Clemente J, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, and Azpiroz F.
    Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.
    Gut. 2014 Mar;63(3):401-8. Decile 1

2013

  1. Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J
    Topoisomerase II regulates yeast genes with singular chromatin architectures
    Nucleic Acids Res. 2013 Nov 1;41(20):9243-56. Decile 1

  2. MetaHIT Consortium. (including Manichanh C.)
    Richness of human gut microbial communities correlates with metabolic markers
    Nature. Aug 29;500(7464):541-6.Decile 1

  3. Varela E, Manichanh C, Gallart M, Torrejon A, Borruel N, Casellas F, Guarner F, Antolin M.
    Colonization by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis
    Aliment Pharmacol Ther. Jul;38(2):151-61.

    4. 2012

    Manichanh C, Borruel N, Casellas F, Gaurner F
    Gut Microbiota and IBD (2012)
    Nature Reviews Gastroenterology & Hepatology (PMID:22907164). ISI-IF: 8.1. Decile 1

    Cardona S, Eck A, Cassellas M, Gallart M, Alastrue C, Dore J, Azpiroz F, Roca J, Guarner F, Manichanh C* (2012)
    Storage conditions of intestinal Microbiota matter in functional metagenomics.
    BMC Microbiology, 12:158. ISI-IF: 3.04

    2011

    Arumugam, M., et al. (including Manichanh C.)
    Enterotypes of the human gut microbiome.
    Nature (full article online April 20, 2011). ISI-IF: 30.9. Decile 1

    2010

    Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al.
    A human gut microbial gene catalogue established by metagenomic sequencing.
    Nature, 464, 59-65 (full article). Cover image. ISI-IF: 30.9. Decile 1

    Manichanh C*, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R and Guarner F
    Reshaping the gut microbiome with bacterial transplantation and antibiotic intake
    Genome Res, 20, 1411-1419 Cover image Highlight in Nature 467, 9 (2010) ISI-IF: 11.3. Decile 1

    2008

    Manichanh C*, Chapple CE, Frangeul L, Gloux K, Guigo R and Dore J
    A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.
    Nucleic Acids Res, 36, 5180-5188 ISI-IF: 7.4. Decile 1

    Manichanh C*, Varela E, Martinez C, Antolin M, Llopis M, Dore J, Giralt J, Guarner F and Malagelada JR
    The gut microbiota predispose to the pathophysiology of acute postradiotherapy diarrhea
    Am J Gastroenterol, 103, 1754-1761 ISI-IF: 6.4. Decile 1

    2007

    Gloux K, Leclerc M, Iliozer H, L'Haridon R, Manichanh C, Corthier G, Nalin R, Blottiere HM and Dore J
    Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth
    Appl Environ Microbiol, 73, 3734-3737 ISI-IF: 3.8

    2006

    Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J and Dore J
    Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
    Gut, 55, 205-211 Leading Article ISI-IF: 9.4. Decile 1

    Seksik P, Sokol H, Lepage P, Vasquez N, Manichanh C, Mangin I, Pochart P, Dore J and Marteau P
    Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease
    Aliment Pharmacol Ther, 24 Suppl 3, 11-18

    2004

    Mougel F, Manichanh C, Duchateau N'guyen G and Termier M
    Genomic choice of codons in 16 microbial species
    J Biomol Struct Dyn, 22, 315-329



    BOOK CHAPTERS


    Doré J, Manichanh C. (2014)
    Chapter title: Techniqes to Characterize the Gut Miceobiota.
    Book title: WGO Handbook on Gut Microbes
    World Gastroenterology Organization (WGO)

    Manichanh C.
    Chapter title: Antibiotics and But Microbes
    Book title: WGO Handbook on Gut Microbes
    World Gastroenterology Organization (WGO)

    Manichanh C, (2011)
    Chapter title: Metagenomic Approaches for bacterial detection and identification
    book title: Molecular Detection of Human Bacterial Pathogens
    Francis and Taylor

    Manichanh C, Chapple C, Frangeul L, Gloux K, Guigo R, Dore J (2011)
    Chapter title: A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic sample book title: Handbook of Molecular Microbial
    Ecology I: Metagenomics and Complementary Approaches
    John Wiley & Sons, Inc



    OTHER CONTRIBUTIONS


    Manichanh C, Mace M, Bonnafous P, Precigout S, Boutolleau D, Gautheret-Dejean A and Agut H (2003). Real-time PCR as a versatile tool for investigating the susceptibility of human herpesvirus 6 to antiviral agents
    Antimicrob Agents Chemother, 47, 3021-3024

    Manichanh C, Olivier-Aubron C, Lagarde JP, Aubin JT, Bossi P, Gautheret-Dejean A, Huraux JM and Agut, H (2001). Selection of the same mutation in the U69 protein kinase gene of human herpesvirus-6 after prolonged exposure to ganciclovir in vitro and in vivo
    J Gen Virol, 82, 2767-2776

    Manichanh C, Grenot P, Gautheret-Dejean A, Debre P, Huraux JM and Agut H (2000)
    Susceptibility of human herpesvirus 6 to antiviral compounds by flow cytometry analysis
    Cytometry, 40, 135-140

    De Bolle L, Michel D, Mertens T, Manichanh C, Agut H, De Clercq E and Naesens L (2002)
    Role of the human herpesvirus 6 u69-encoded kinase in the phosphorylation of ganciclovir
    Mol Pharmacol, 62, 714-721

    Fernandez C, Boutolleau D, Manichanh C, Mangeney N, Agut H and Gautheret-Dejean A (2002)
    Quantitation of HHV-7 genome by real-time polymerase chain reaction assay using MGB probe technology
    J Virol Methods, 106, 11-16

    Gautheret-Dejean A, Manichanh C, Thien-Ah-Koon F, Fillet AM, Mangeney N, Vidaud M, Dhedin N, Vernant JP and Agut H (2002)
    Development of a real-time polymerase chain reaction assay for the diagnosis of human herpesvirus-6 infection and application to bone marrow transplant patients
    J Virol Methods, 100, 27-35