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  • 1.
    Adamovic, Tatjana
    et al.
    Med Coll Wisconsin, Human & Mol Genet Ctr, Milwaukee, WI 53226 USA.
    Hamta, Achmad
    Univ Gothenburg, CMB Genet, Gothenburg, Sweden.
    Roshani, Leyla
    Univ Gothenburg, CMB Genet, Gothenburg, Sweden.
    Lü, Xuschun
    Univ Gothenburg, CMB Genet, Gothenburg, Sweden.
    Röhme, Dan
    Univ Gothenburg, CMB Genet, Gothenburg, Sweden.
    Helou, Khalil
    Univ Gothenburg, Dept Oncol, Gothenburg, Sweden.
    Klinga-Levan, Karin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Levan, Göran
    Univ Gothenburg, CMB Genet, Gothenburg, Sweden.
    Rearrangement and allelic imbalance on chromosome 5 leads to homozygous deletions in the CDKN2A/2B tumor suppressor gene region in rat endometrial cancer2008In: Cancer Genetics and Cytogenetics, ISSN 0165-4608, E-ISSN 1873-4456, Vol. 184, no 1, 9-21 p.Article in journal (Refereed)
    Abstract [en]

    The inbred BDII rat is a valuable experimental model for the genetic analysis of hormone-dependent endometrial adenocarcinoma (EAC). One common aberration detected previously by comparative genomic hybridization in rat EAC is loss affecting mostly the middle part of rat chromosome 5 (RNO5). First, we applied an RNO5-specific painting probe and four region-specific gene probes onto tumor cell metaphases from 21 EACs, and found that rearrangements involving RNO5 were common. The copy numbers of loci situated on RNO5 were found to be reduced, particularly for the CDKN2A/2B locus. Second, polymerase chain reaction analysis was performed with 22 genes and markers and homozygous deletions of the CDKN2A exon 1β and CDKN2B genes were detected in 13 EACs (62%) and of CDKN2A exon 1α in 12 EACs (57%) Third, the occurrence of allelic imbalance in RNO5 was analyzed using 39 microsatellite markers covering the entire chromosome and frequent loss of heterozygosity was detected. Even more intriguing was the repeated finding of allele switching in a narrow region of 7 Mb across the CDKN2A/2B locus. We conclude that genetic events affecting the middle part of RNO5 (including bands 5q31q33 and the CDKN2A locus) contribute to the development of EAC in rat, with the CDKN2A locus having a primary role.

  • 2.
    Enroth, Helena
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Unilabs AB.
    Engstrand, L
    Karolinska Institute and Science for Life Laboratory.
    Infectious Diseases: Helicobacter pylori2015In: Reference Module in Biomedical Sciences, Elsevier, 2015Chapter in book (Other academic)
    Abstract [en]

    Abstract Helicobacter pylori infection is one of the most common human infections in the world. The bacteria cause peptic ulcer disease and their infection is an important factor for gastric cancer development. The bacteria are transmitted from person to person within families, with young children most often infected. The bacteria reside in the stomach for a lifetime if untreated by antimicrobial agents. Many virulence factors are known that contribute to the persistence of the bacteria in the stomach, and the bacteria harbors a pathogenicity island in its genome. The discovery of H. pylori as a cause of gastritis in the stomach led to the Nobel Prize in Physiology or Medicine 2005.

  • 3.
    Karlsson, Diana
    et al.
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Ljungström, Lars
    Department of Infectious Diseases- Skaraborg Hospital, Skövde, Sweden.
    Multimarker approach for sepsis diagnostics2015In: 25th European Congress of Clinical Mircobiology and Infectious Diseases, Copenhagen, April 25-28, 2015, European Society of ClinicalMicrobiology and Infectious Diseases (ESCMID) , 2015Conference paper (Refereed)
    Abstract [en]

    OBJECTIVES

    The aim of this study was to assess the performance of a multimarker model in distinguishing patients with sepsis from those with non-infective systemic inflammatory response.

    METHODS

    This study is part of a prospective study of community-onset severe sepsis and septic shock in adults conducted from September 2011 to June 2012 at Skaraborg Hospital, in the western region of Sweden. The levels of 92 inflammation-related human protein biomarkers were measured simultaneously using Proseek® Multiplex Inflammation I96x96 (Olink Bioscience, Sweden) in 122 plasma samples collected from patients suspected with sepsis. After pre-processing normalization procedure, measurements of the markers were obtained as Normalized Protein eXpression (NPX) units on a log2 scale (GenEx, MultiD Analyses AB, Sweden). The study was approved by the Regional Ethical Review Board of Gothenburg (376-11). All patients enrolled provided written informed consent.

    To reduce the number of markers, factor analysis was performed. Thereafter, a multimarker model for classification was derived using discriminant analysis. The multimarker model consisted of a linear function of the selected markers. Cross-validation was performed by classifying each sample by the discriminant function derived from all samples other than that specific sample. The performance was assessed as area under receiving operating characteristic (ROC) curve. The cut-off for sensitivity and specificity was derived from the cut score of the discriminant function. Statistical analyses were performed in SPSS 22.0 (IBM Corporation Somers, NY USA).

    RESULTS

    Of the 122 samples, 80 (66%) were from patients diagnosed with sepsis and 42 from patients with non-infective systemic inflammatory response syndrome (SIRS). The five markers selected for the multimarker model were interleukin-6 (IL-6), cystatin D (CST5), delta and notch-like epidermal growth factor-related receptor (DNER), STAM-binding protein (STAMPB), macrophage colony-stimulating factor 1 (CSF 1). Every single marker was statistically different between the groups (p value < 0.001), except for DNER (p value 0.064) and STAMPB (p value 0.060). The area under ROC was higher for the multimarker model (81%) than for each biomarker separately (Figure 1). The accuracy for the multimarker model was 72% [64-80, 95% CI]; sensitivity 84% [77-91, 95% CI]; specificity 60% [51-69, 95% CI]; positive predictive value 79% [72-86, 95% CI]; and negative predictive value 66% [58-74, 95% CI].

    CONCLUSION

    A higher power of discrimination is obtained by combining more than one biomarker. However, the multimarker candidates identified in this study need further assessment.

  • 4.
    Kjellerås, Jennifer
    University of Skövde, School of Life Sciences.
    1,25(OH)2D3 increase caspase-3 activity in LNCaP cells after 2 minutes and 48h separately2007Independent thesis Basic level (degree of Bachelor), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Cancer or malignant tumors has a high death frequency in many countries. Nowadays many research facilities are dedicated to find new substances and techniques which would lead to better cancer therapies. Seven years ago a research team from Finland made a remarkable connection between vitamin D deficiencies and an increased chance of getting prostate cancer. The research investigating this statement has lead to findings of a new non-classical effect of the calcium controlling vitamin, 1,25(OH)2D3. This effect involves anti-proliferatory effects and more importantly apoptotic effects resulting in the hope of finding a new drug that can cure prostate cancer with the smallest amount of harm to the body.

    In an attempt to find out if the signalling pathway of this apoptotic effect is fast or slow, an experiment designed to detect when the apoptotic protein caspase-3 is induced has been performed. Cells from the cell line LNCaP has been cultured and incubated with 1,25(OH)2D3 and after 0min - 48h an assay was performed to detect the relative amounts of caspase-3 present in every sample. The optimal time period (48h) was then subjected to three different concentrations of 1,25(OH)2D3 and read in the same way as the previous samples. The results showed an increase in caspase-3 expression as early as 2 min, but disappear to be seen again at 24h and are more profound in 48h samples. The caspase-3 expression was also seen to form a possible exponential curve in dose-response.

  • 5.
    Ljungström, Lars R.
    et al.
    Department of Infectious Diseases, Skaraborg Hospital / CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg.
    Jacobsson, Gunnar
    Department of Infectious Diseases, Skaraborg Hospital, Skövde / CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg.
    Claesson, Berndt E. B.
    Department of Clinical Microbiology, Unilabs, Skaraborg Hospital, Skövde.
    Andersson, Rune
    CARe (Center for Antibiotic Resistance Research), Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy at Gothenburg University, Gothenburg, Sweden.
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Molecular Microbiology, Unilabs, Skaraborg Hospital, Skövde.
    Respiratory viral infections are underdiagnosed in patients with suspected sepsis2017In: European Journal of Clinical Microbiology and Infectious Diseases, ISSN 0934-9723, E-ISSN 1435-4373, Vol. 36, no 10, 1767-1776 p.Article in journal (Refereed)
    Abstract [en]

    The study aim was to investigate the prevalence and clinical relevance of viral findings by multiplex PCR from the nasopharynx of clinically septic patients during a winter season. During 11 weeks of the influenza epidemic period in January-March 2012, consecutive adult patients suspected to be septic (n = 432) were analyzed with cultures from blood and nasopharynx plus multiplex PCR for respiratory viruses on the nasopharyngeal specimen. The results were compared with those from microbiology analyses ordered as part of standard care. During the winter season, viral respiratory pathogens, mainly influenza A virus, human metapneumovirus, coronavirus, and respiratory syncytial virus were clinically underdiagnosed in 70% of patients positive by the multiplex PCR assay. During the first four weeks of the influenza epidemic, few tests for influenza were ordered by clinicians, indicating low awareness that the epidemic had started. Nasopharyngeal findings of Streptococcus pneumoniae and Haemophilus influenzae by culture correlated to pneumonia diagnosis, and in those patients laboratory signs of viral co-infections were common but rarely suspected by clinicians. The role of respiratory viral infections in patients presenting with a clinical picture of sepsis is underestimated. Specific antiviral treatment might be beneficial in some cases and may reduce spread in a hospital setting. Diagnosing viral infections may promote reduction of unnecessary antibiotic use. It can also be a tool for decisions concerning patient logistics, in order to minimize exposure of susceptible patients and personnel.

  • 6.
    Magnusson, Maria K.
    et al.
    Department of Microbiology and Immunology, University of Gothenburg, Institute for Biomedicine, Gothenburg, Sweden / Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Institute for Medicine, Gothenburg, Sweden.
    Strid, Hans
    Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Institute for Medicine, Gothenburg, Sweden / Södra Älvsborg Hospital, Department of Internal Medicine, Borås, Sweden.
    Sapnara, Maria
    Department of Microbiology and Immunology, University of Gothenburg, Institute for Biomedicine, Gothenburg, Sweden / Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Institute for Medicine, Gothenburg, Sweden.
    Lasson, Anders
    Södra Älvsborg Hospital, Department of Internal Medicine, Borås, Sweden.
    Bajor, Antal
    Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Institute for Medicine, Gothenburg, Sweden / Södra Älvsborg Hospital, Department of Internal Medicine, Borås, Sweden .
    Ung, Kjell-Arne
    Kärnsjukhuset, Department of Internal Medicine, Skövde, Sweden.
    Öhman, Lena
    University of Skövde, School of Health and Education. Department of Microbiology and Immunology, University of Gothenburg, Institute for Biomedicine, Gothenburg, Sweden / Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Institute for Medicine, Gothenburg, Sweden.
    Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition2016In: Journal of Crohn's & Colitis, ISSN 1873-9946, E-ISSN 1876-4479, Vol. 10, no 8, 943-952 p.Article in journal (Refereed)
    Abstract [en]

    BACKGROUND AND AIMS: Anti-tumour necrosis factor [TNF] therapy is used in patients with ulcerative colitis [UC], but not all patients respond to treatment. Antimicrobial peptides [AMPs] and the gut microbiota are essential for gut homeostasis and may be important for treatment outcome. The aim of this study was to determine AMP and microbiota profiles in patients with UC before anti-TNF therapy start and correlate these data to treatment outcome.

    METHODS: Serum and biopsies were obtained from UC patients naïve to biological therapy [n = 56] before anti-TNF therapy start [baseline]. Fecal samples were taken at baseline and Weeks 2 and 6. Quantitative proteomic analysis was performed in mucosal biopsies. Expression of AMPs and cytokines was determined in biopsies and serum. Microbiota analysis of fecal samples was performed using GA-map™ Dysbiosis Test and real-time quantitative polymerase chain reaction [rtPCR]. Treatment response was evaluated 12-14 weeks after baseline.

    RESULTS: At baseline, proteomic analysis of biopsies showed that treatment responders and non-responders had differential expression of AMPs. Eleven AMP and AMP-related genes were analysed by rtPCR in mucosal biopsies and could together discriminate responders from non-responders at baseline. The most important nominators for response were increased expression of defensin 5 and eosinophilic cationic protein. Microbiota analysis revealed lower dysbiosis indexes and higher abundance of Faecalibacterium prausnitzii in responders compared with non-responders at baseline. Also, abundance of F. prausnitzii increased during induction therapy in responders.

    CONCLUSIONS: Anti-TNF therapy responders and non-responders display distinctly separate patterns of mucosal AMP expression and gut microbiota before treatment start. This indicates that intestinal antimicrobial/microbial composition can influence treatment outcome.

  • 7. Nordlander, Carola
    et al.
    Samuelsson, Emma
    Klinga-Levan, Karin
    University of Skövde, School of Life Sciences.
    Behboudi, Afrouz
    Recurrent Chromosome 10 Aberrations and Tp53 Mutations in Rat Endometrial Adenocarcinomas2008In: Advances in Experimental Medicine and Biology, ISSN 0065-2598, Vol. 617, 519-525 p.Article in journal (Refereed)
    Abstract [en]

    Human genetic heterogeneity and differences in the environment and life style make analysis of complex diseases such as cancer difficult. By using inbred animal strains, the genetic variability can be minimized and the environmental factors can be reasonably controlled. Endometrial adenocarcinoma (EAC) is the most common gynecologic malignancy, ranking fourth in incidence among tumors in women. The inbred BDII rat strain is genetically prone to spontaneously develop hormone-related EAC, and can be used as a tool to investigate and characterize genetic changes in this tumor type. In the present project, BDII females were crossed to males from two nonsusceptible rat strains and F1, F2, and backcross progeny were produced. Genetic and molecular genetic analysis of tumors showed that rat chromosome 10 (RNO10) was frequently involved in genetic changes. Our data indicate that often there was loss of chromosomal material in the proximal to middle part of the chromosome followed by gains in distal RNO10. This suggested that there is a tumor suppressor gene(s) in the proximal to middle part of RNO10 and an oncogene(s) in the distal part of the chromosome with potential significance in EAC development. The Tp53 gene, located at band RNO10q24-q25, was a strong candidate target for the observed aberrations affecting the middle part of the chromosome. However, our Tp53 gene mutation analyses suggested that a second gene situated very close to Tp53 might be the main target for the observed pattern of genetic changes.

  • 8.
    Owemyr, Ida
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
    Enroth, Helena
    Unilabs AB, Skövde.
    Ljungström, Lars
    Kärnsjukhuset, Skövde.
    Pernestig, Anna-Karin
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Karlsson, Diana
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Utvärdering av microarray-baserad plattform för snabb identifiering av patogener hos patienter med misstänkt sepsis2012Conference paper (Refereed)
  • 9.
    Rai, Vijeta
    University of Skövde, School of Bioscience.
    Screening of large collection of compounds for anti-human parainfluenza virus type-2 activity and evaluation of hit compounds2017Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Human parainfluenza virus type-2 (HPIV-2) is a highly contagious respiratory pathogen that can cause severe respiratory disease known as laryngotracheobronchitis or croup-like disease in children. No specific vaccine or an antiviral drug is currently approved for treatment of HPIV-2 infections. In this project, a library of 14400 diverse compounds had been screened for anti-HPIV-2 activities in cultures of African green monkey kidney cells. All compounds that inhibited the virus induced syncytium-forming activity in these cells were considered as hit compounds. Three hit compounds showed moderate anti-HPIV-2 activity characterized by the IC50 values of 20 µM and selectivity indices of approximately 5. This suggests that the antiviral activity of these compounds was due to targeting activities of cellular rather than viral components. Another hit compound, referred to as compound 5, showed anti-HPIV-2 activity that was manifested as a reduction of area of the virus-induced plaques in cells at not cytotoxic concentrations. Interestingly, this compound did not inhibit initial infection nor the virus production in infected cells as revealed by the time-of-addition assay. Moreover, it showed no direct the virus-inactivating (virucidal activity) against HPIV-2 particles. However, relatively short pre-treatment (4 hours) of the cells with compound 5 prior to the virus infection was sufficient for its plaque size-reducing activity suggesting that anti-HPIV-2 activity of compound 5 was due to targeting activities of cellular rather than viral components. Further studies are needed to elucidate the anti-HPIV-2 mechanism of activity of hit compounds identified in the present study.

  • 10.
    Retz, Karolina
    et al.
    Department of Clinical Microbiology, Unilabs AB, Skövde.
    Andersson, Sofie
    Department of Clinical Microbiology, Unilabs AB, Skövde .
    Andersson, Carl
    University of Skövde.
    Svensson, Kristina
    Department of Clinical Microbiology, Unilabs AB, Skövde .
    Ljungström, Lars
    The Skaraborg Hospital, Skövde, Sweden .
    Enroth, Helena
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Microbiology, Unilabs AB, Skövde .
    Tilevik, Diana
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Pernestig, Anna-Karin
    University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre.
    Evaluation of the QuickFISH and the Sepsityper assays for early identification of etiological agents in bloodstream infection in a clinical routine setting2017Conference paper (Refereed)
  • 11.
    Suzuki, Kazushi
    et al.
    Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA.
    Wang, Xin
    Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA.
    Weilbacher, Thomas
    Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA.
    Pernestig, Anna-Karin
    Microbiology and Tumorbiology Center, Karolinska Institutet, Stockholm, Sweden.
    Melefors, Öjar
    Microbiology and Tumorbiology Center, Karolinska Institutet, Stockholm, Sweden.
    Georgellis, Dimitris
    Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
    Babitzke, Paul
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
    Romeo, Tony
    Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA.
    Regulatory circuitry of the CsrA/CsrB and BarA/UvrY systems of Escherichia coli2002In: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 184, no 18, 5130-5140 p.Article in journal (Refereed)
    Abstract [en]

    The global regulator CsrA (carbon storage regulator) is an RNA binding protein that coordinates centralcarbon metabolism, activates flagellum biosynthesis and motility, and represses biofilm formation in Escherichiacoli. CsrA activity is antagonized by the untranslated RNA CsrB, to which it binds and forms a globularribonucleoprotein complex. CsrA indirectly activates csrB transcription, in an apparent autoregulatory mechanism.In the present study, we elucidate the intermediate regulatory circuitry of this system. Mutationsaffecting the BarA/UvrY two-component signal transduction system decreased csrB transcription but did notaffect csrA-lacZ expression. The uvrY defect was severalfold more severe than that of barA. Both csrA and uvrYwere required for optimal barA expression. The latter observation suggests an autoregulatory loop for UvrY.Ectopic expression of uvrY suppressed the csrB-lacZ expression defects caused by uvrY, csrA, or barA mutations;csrA suppressed csrA or barA defects; and barA complemented only the barA mutation. Purified UvrY proteinstimulated csrB-lacZ expression approximately sixfold in S-30 transcription-translation reactions, revealing adirect effect of UvrY on csrB transcription. Disruption of sdiA, which encodes a LuxR homologue, decreased theexpression of uvrY-lacZ and csrB-lacZ fusions but did not affect csrA-lacZ. The BarA/UvrY system activatedbiofilm formation. Ectopic expression of uvrY stimulated biofilm formation by a csrB-null mutant, indicative ofa CsrB-independent role for UvrY in biofilm development. Collectively, these results demonstrate that uvrYresides downstream from csrA in a signaling pathway for csrB and that CsrA stimulates UvrY-dependentactivation of csrB expression by BarA-dependent and -independent mechanisms.

  • 12.
    Tap, Julien
    et al.
    Danone Nutricia Research, Palaiseau, France / French National Institute for Agricultural Research (INRA) MetaGenoPolis, Jouy en Josas, France.
    Derrien, Muriel
    Danone Nutricia Research, Palaiseau, France.
    Törnblom, Hans
    Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden / Centre for Person-Centered Care, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
    Brazeilles, Rémi
    Danone Nutricia Research, Palaiseau, France.
    Cools-Portier, Stéphanie
    Danone Nutricia Research, Palaiseau, France.
    Doré, Joël
    French National Institute for Agricultural Research (INRA) MetaGenoPolis, Jouy en Josas, France.
    Störsrud, Stine
    Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
    Le Nevé, Boris
    Danone Nutricia Research, Palaiseau, France.
    Öhman, Lena
    University of Skövde, School of Health and Education. Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden / Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
    Simrén, Magnus
    Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden / Centre for Person-Centered Care, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden / Center for Functional GI and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina, USA.
    Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome2017In: Gastroenterology, ISSN 0016-5085, E-ISSN 1528-0012, Vol. 152, no 1, 111-123.e8 p.Article in journal (Refereed)
    Abstract [en]

    BACKGROUND & AIMS: We have limited knowledge about the association between the composition of the intestinal microbiota and clinical features of irritable bowel syndrome (IBS). We collected information on the fecal and mucosa-associated microbiota of patients with IBS and evaluated whether these were associated with symptoms.

    METHODS: We collected fecal and mucosal samples from adult patients who met the Rome III criteria for IBS at secondary or tertiary care outpatient clinics in Sweden, as well as from healthy subjects. The exploratory set comprised 149 subjects (110 with IBS and 39 healthy subjects); 232 fecal samples and 59 mucosal biopsy samples were collected and analyzed by 16S ribosomal RNA targeted pyrosequencing. The validation set comprised 46 subjects (29 with IBS and 17 healthy subjects); 46 fecal samples, but no mucosal samples, were collected and analyzed. For each subject, we measured exhaled H2 and CH4, oro-anal transit time, and the severity of psychological and gastrointestinal symptoms. Fecal methanogens were measured by quantitative polymerase chain reaction. Numeric ecology analyses and a machine learning procedure were used to analyze the data.

    RESULTS: Fecal microbiota showed covariation with mucosal adherent microbiota. By using classic approaches, we found no differences in fecal microbiota abundance or composition between patients with vs without IBS. A computational statistical technique-like machine learning procedure allowed us to reduce the 16S ribosomal RNA data complexity into a microbial signature for severe IBS, consisting of 90 bacterial operational taxonomic units. We confirmed the robustness of the intestinal microbial signature for severe IBS in the validation set. The signature was able to discriminate between patients with severe symptoms, patients with mild/moderate symptoms, and healthy subjects. By using this intestinal microbiota signature, we found IBS symptom severity to be associated negatively with microbial richness, exhaled CH4, presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species. This microbiota signature could not be explained by differences in diet or use of medications.

    CONCLUSIONS: In analyzing fecal and mucosal microbiota from patients with IBS and healthy individuals, we identified an intestinal microbiota profile that is associated with the severity of IBS symptoms.

    TRIAL REGISTRATION NUMBER: NCT01252550.

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