1
|
Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB. Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nat Commun 2024; 15:1791. [PMID: 38424056 PMCID: PMC10904388 DOI: 10.1038/s41467-024-46033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
Collapse
Affiliation(s)
- Paula Istvan
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Einar Birkeland
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ekaterina Avershina
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Vahid Bemanian
- Pathology Department, Akershus University Hospital, Lørenskog, Norway
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Sonia Tarallo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Trine B Rounge
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
| |
Collapse
|
2
|
Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
| |
Collapse
|
3
|
Avershina E, Frye SA, Ali J, Taxt AM, Ahmad R. Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Front Microbiol 2022; 13:822402. [PMID: 35369431 PMCID: PMC8970966 DOI: 10.3389/fmicb.2022.822402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Stephan A Frye
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Arne M Taxt
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
4
|
Khezri A, Avershina E, Ahmad R. Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates. Microorganisms 2021; 9:microorganisms9122560. [PMID: 34946161 PMCID: PMC8704702 DOI: 10.3390/microorganisms9122560] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/28/2022] Open
Abstract
Emerging new sequencing technologies have provided researchers with a unique opportunity to study factors related to microbial pathogenicity, such as antimicrobial resistance (AMR) genes and virulence factors. However, the use of whole-genome sequence (WGS) data requires good knowledge of the bioinformatics involved, as well as the necessary techniques. In this study, a total of nine Escherichia coli and Klebsiella pneumoniae isolates from Norwegian clinical samples were sequenced using both MinION and Illumina platforms. Three out of nine samples were sequenced directly from blood culture, and one sample was sequenced from a mixed-blood culture. For genome assembly, several long-read, (Canu, Flye, Unicycler, and Miniasm), short-read (ABySS, Unicycler and SPAdes) and hybrid assemblers (Unicycler, hybridSPAdes, and MaSurCa) were tested. Assembled genomes from the best-performing assemblers (according to quality checks using QUAST and BUSCO) were subjected to downstream analyses. Flye and Unicycler assemblers performed best for the assembly of long and short reads, respectively. For hybrid assembly, Unicycler was the top-performing assembler and produced more circularized and complete genome assemblies. Hybrid assembled genomes performed substantially better in downstream analyses to predict putative plasmids, AMR genes and β-lactamase gene variants, compared to MinION and Illumina assemblies. Thus, hybrid assembly has the potential to reveal factors related to microbial pathogenicity in clinical and mixed samples.
Collapse
Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
| | - Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
- Faculty of Health Sciences, Institute of Clinical Medicine, UiT-The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway
- Correspondence:
| |
Collapse
|
5
|
Avershina E, Shapovalova V, Shipulin G. Fighting Antibiotic Resistance in Hospital-Acquired Infections: Current State and Emerging Technologies in Disease Prevention, Diagnostics and Therapy. Front Microbiol 2021; 12:707330. [PMID: 34367112 PMCID: PMC8334188 DOI: 10.3389/fmicb.2021.707330] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 12/20/2022] Open
Abstract
Rising antibiotic resistance is a global threat that is projected to cause more deaths than all cancers combined by 2050. In this review, we set to summarize the current state of antibiotic resistance, and to give an overview of the emerging technologies aimed to escape the pre-antibiotic era recurrence. We conducted a comprehensive literature survey of >150 original research and review articles indexed in the Web of Science using "antimicrobial resistance," "diagnostics," "therapeutics," "disinfection," "nosocomial infections," "ESKAPE pathogens" as key words. We discuss the impact of nosocomial infections on the spread of multi-drug resistant bacteria, give an overview over existing and developing strategies for faster diagnostics of infectious diseases, review current and novel approaches in therapy of infectious diseases, and finally discuss strategies for hospital disinfection to prevent MDR bacteria spread.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Laboratory or Postgenomic Technologies, Izmerov Research Institute of Occupational Health, Moscow, Russia
| | - Valeria Shapovalova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Centre for Strategic Planning of FMBA of Russia, Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Centre for Strategic Planning of FMBA of Russia, Moscow, Russia
| |
Collapse
|
6
|
Schei K, Avershina E, Øien T, Rudi K, Follestad T, Salamati S, Ødegård RA. Correction to: Early gut mycobiota and mother-offspring transfer. Microbiome 2021; 9:120. [PMID: 34020715 PMCID: PMC8140462 DOI: 10.1186/s40168-021-01094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Kasper Schei
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway.
| | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, NMBU - Norway University of Life Sciences, Ås, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, NMBU - Norway University of Life Sciences, Ås, Norway
| | - Turid Follestad
- Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Saideh Salamati
- ObeCe - Regional Centre for Obesity Research and Innovation, St. Olav's University Hospital, Trondheim, Norway
| | - Rønnaug Astri Ødegård
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
- ObeCe - Regional Centre for Obesity Research and Innovation, St. Olav's University Hospital, Trondheim, Norway
| |
Collapse
|
7
|
Avershina E, Sharma P, Taxt AM, Singh H, Frye SA, Paul K, Kapil A, Naseer U, Kaur P, Ahmad R. AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae. Comput Struct Biotechnol J 2021; 19:1896-1906. [PMID: 33897984 PMCID: PMC8060595 DOI: 10.1016/j.csbj.2021.03.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours. In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network. Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1–8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Arne M Taxt
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Harpreet Singh
- Informatics, System and Research Management, Indian Council of Medical Research, New Delhi, India
| | - Stephan A Frye
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Kolin Paul
- Department of Computer Science & Engineering, IIT Delhi, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Umaer Naseer
- Department of Zoonotic, Food- and Waterborne Infections, 0213 Oslo, Norwegian Institute of Public Health, Oslo, Norway
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Institute of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway
| |
Collapse
|
8
|
Khezri A, Avershina E, Ahmad R. Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates. Microorganisms 2020; 9:E52. [PMID: 33375502 PMCID: PMC7823326 DOI: 10.3390/microorganisms9010052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/29/2022] Open
Abstract
Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results.
Collapse
Affiliation(s)
- Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
| | - Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
- Laboratory or Postgenomic Technologies, Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, 2318 Hamar, Norway; (A.K.); (E.A.)
- Division of Medical Services-Clinical Microbiology, Inland Hospital, 2609 Lillehammer, Norway
- Institute of Clinical Medicine, Faculty of Health Sciences, UiT—The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway
| |
Collapse
|
9
|
Schei K, Simpson MR, Avershina E, Rudi K, Øien T, Júlíusson PB, Underhill D, Salamati S, Ødegård RA. Early Gut Fungal and Bacterial Microbiota and Childhood Growth. Front Pediatr 2020; 8:572538. [PMID: 33240830 PMCID: PMC7680752 DOI: 10.3389/fped.2020.572538] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/07/2020] [Indexed: 12/27/2022] Open
Abstract
Introduction: Childhood growth is a sensitive marker of health. Animal studies show increased height and weight velocity in the presence of fungal as well as antibiotic supplement in feed. Human studies on early gut microbiota and anthropometrics have mainly focused on bacteria only and overweight, with diverging results. We thus aimed to investigate the associations between childhood growth [height and body mass index (BMI)] and early fungal and bacterial gut microbiota. Methods: In a population-based cohort, a subset of 278 pregnant mothers was randomized to drink milk with or without probiotic bacteria during and after pregnancy. We obtained fecal samples in offspring at four time points between 0 and 2 years and anthropometric measurements 0 and 9 years. By quantitative PCR and 16S/ITS rRNA gene sequencing, children's gut microbiota abundance and diversity were analyzed against height standard deviation score (SDS) and BMI-SDS and presented as effect estimate (β) of linear mixed models. Results: From 278 included children (149 girls), 1,015 fecal samples were collected. Maternal probiotic administration did not affect childhood growth, and the groups were pooled. Fungal abundance at 2 years was positively associated with height-SDS at 2-9 years (β = 0.11 height-SDS; 95% CI, 0.00, 0.22) but not with BMI-SDS. Also, higher fungal abundance at 1 year was associated with a lower BMI-SDS at 0-1 year (β = -0.09 BMI-SDS; 95% CI, -0.18, -0.00), and both bacterial abundance and bacterial alpha diversity at 1 year were associated with lower BMI-SDS at 0-1 year (β = -0.13 BMI-SDS; 95% CI, -0.22, -0.04; and β = -0.19 BMI-SDS; 95% CI, -0.39, -0.00, respectively). Conclusions: In this prospective cohort following 0-9-year-old children, we observed that higher gut fungal abundances at 2 years were associated with taller children between 2 and 9 years. Also, higher gut fungal and bacterial abundances and higher gut bacterial diversity at 1 year were associated with lower BMI in the first year of life. The results may indicate interactions between early gut fungal microbiota and the human growth-regulating physiology, previously not reported. Clinical Trial Registration: Clinicaltrials.gov, NCT00159523.
Collapse
Affiliation(s)
- Kasper Schei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Melanie Rae Simpson
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Ekaterina Avershina
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Pétur Benedikt Júlíusson
- Department of Health Registries, Norwegian Institute of Public Health, Bergen, Norway.,Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - David Underhill
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Division of Immunology Research, Cedars-Sinai, Los Angeles, CA, United States
| | - Saideh Salamati
- Regional Centre of Obesity Research and Innovation (ObeCe), Trondheim University Hospital, Trondheim, Norway
| | - Rønnaug Astri Ødegård
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Regional Centre of Obesity Research and Innovation (ObeCe), Trondheim University Hospital, Trondheim, Norway
| |
Collapse
|
10
|
Ravi A, Avershina E, Angell IL, Ludvigsen J, Manohar P, Padmanaban S, Nachimuthu R, Snipen L, Rudi K. Comparison of reduced metagenome and 16S rRNA gene sequencing for determination of genetic diversity and mother-child overlap of the gut associated microbiota. J Microbiol Methods 2018; 149:44-52. [PMID: 29501688 DOI: 10.1016/j.mimet.2018.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Use of the 16S rRNA gene in microbiota studies is limited by the lack of taxonomic and functional resolution. High resolution analyses are particularly important for understanding transmission and persistence of bacteria. The aim of our work was therefore to compare a novel reduced metagenome sequencing (RMS) approach with 16S rRNA gene sequencing to determine both the metagenome genetic diversity and the mother-to-child sharing of the microbiota in a cohort of 17 mother-child pairs. We found that although both approaches gave comparable results with respect to sample separation and taxonomy, RMS gave higher resolution and the potential for genomic-/functional assignment. Using RMS we estimated that the metagenome size increased from about 60 Mbp for 4-day-old children to about 225 Mbp for mothers. The 4-day-old children shared 7% of the metagenome sequences with the mothers, while the metagenome sequence sharing was >30% among the mothers. We found 15 genomes shared across >50% of the mothers, of which 10 belonged to Clostridia. Only Bacteroides showed a direct mother-child association, with B. vulgatus being abundant in both 4-day-old children and mothers. For the functional assignments, we identified a significant association between antibiotic usage during labor, and quantity of Fosfomycin resistance genes. In conclusion, our results show a higher functional and taxonomic resolution for RMS compared to 16S rRNA gene sequencing, where RMS enabled a detailed description of mother to child gut microbiota transmission - supporting a late recruitment of most gut bacteria and an effect of antibiotic treatment during labor on infant antibiotic resistance gene patterns.
Collapse
Affiliation(s)
- Anuradha Ravi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Ekaterina Avershina
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Inga Leena Angell
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Jane Ludvigsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Prasanth Manohar
- Antibiotic Resistance and Phage Therapy Laboratory, Department of Biomedical Sciences, School of Bioscience and Technology, Vellore Institute of Technology, Tamil Nadu, India
| | | | - Ramesh Nachimuthu
- Antibiotic Resistance and Phage Therapy Laboratory, Department of Biomedical Sciences, School of Bioscience and Technology, Vellore Institute of Technology, Tamil Nadu, India
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| |
Collapse
|
11
|
Avershina E, Slangsvold S, Simpson MR, Storrø O, Johnsen R, Øien T, Rudi K. Diversity of vaginal microbiota increases by the time of labor onset. Sci Rep 2017; 7:17558. [PMID: 29242550 PMCID: PMC5730599 DOI: 10.1038/s41598-017-17972-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/04/2017] [Indexed: 01/09/2023] Open
Abstract
Vaginal microbiota is an important early source of bacterial colonization for newborns. However, only a few small studies have investigated the composition of vaginal microbiota during labor. In this work, we analyzed vaginal swabs collected at 36 weeks gestation and at the onset of labor from 256 women participating in a randomized placebo-controlled study of probiotic supplementation for the prevention of atopic dermatitis in offspring. Although individuals' vaginal microbiota was stable over time, several bacterial families, which are characteristic of mixed community state type (CST) IV, were overrepresented in vaginal swabs sampled at labor. Alpha-diversity also tended to increase by between 36 weeks gestation and the onset of birth. In the majority of women, CST remained the same throughout the study. Among the women who switched their vaginal microbiota from one CST to another, approximately half shifted towards CST IV. Although CST IV is often associated with bacterial vaginosis, which in turn may lead to preterm birth, in our cohort this shift was not associated with self-reported vaginosis, preterm delivery or birthweight. Probiotic consumption did not alter vaginal microbiota.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.
| | - Silje Slangsvold
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - Melanie Rae Simpson
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Ola Storrø
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| |
Collapse
|
12
|
Simpson MR, Avershina E, Storrø O, Johnsen R, Rudi K, Øien T. Breastfeeding-associated microbiota in human milk following supplementation with Lactobacillus rhamnosus GG, Lactobacillus acidophilus La-5, and Bifidobacterium animalis ssp. lactis Bb-12. J Dairy Sci 2017; 101:889-899. [PMID: 29248229 DOI: 10.3168/jds.2017-13411] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/17/2017] [Indexed: 12/20/2022]
Abstract
Breastfeeding is one of the major factors affecting the early development of the infant gut microbiota, and weaning is associated with a shift in the gut microbiota toward a more adult composition. Through breastfeeding, infants receive bioactive components that shape their microbiota while also being exposed to the breast milk and breast surface microbial communities. Recent studies have suggested the possibility of an entero-mammary route of microbial transfer, opening the possibility of infant gut microbiota modulation through maternal probiotic supplementation. In this study, we have analyzed breast milk samples collected at 10 d and 3 mo postpartum from women participating in the Probiotics in the Prevention of Allergy among Children in Trondheim placebo controlled trial. Women who were randomized to the probiotic arm of the Probiotics in the Prevention of Allergy among Children in Trondheim trial received a fermented milk supplemented with Lactobacillus rhamnosus GG, Lactobacillus acidophilus La-5, and Bifidobacterium animalis ssp. lactis Bb-12, consuming this daily from 4 wk before their expected due date until 3 mo after birth. In total, 472 breast milk samples were assessed for the administered bacteria using quantitative real-time PCR and the microbiota transferred during breastfeeding was analyzed using 16S ribosomal RNA gene sequencing of 142 samples. We found that breastfeeding is unlikely to be a significant source of L. rhamnosus GG, L. acidophilus La-5, and B. animalis ssp. lactis Bb-12 for infants in the probiotic arm of the trial. Furthermore, maternal supplementation did not significantly affect the overall composition of the breast milk microbiota transferred during breastfeeding. We also present a descriptive analysis of this microbiota, which was largely dominated by Streptococcus and Staphylococcus genera at both 10 d and 3 mo postpartum. Samples collected at 3 mo postpartum had a statistically significant lower presence and relative abundance of the Staphylococcus genus. These samples also had a greater number of observed species and diversity, including more operational taxonomic units from the Rothia, Veillonella, Granulicatella, and Methylbacterium genera.
Collapse
Affiliation(s)
- Melanie Rae Simpson
- Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, N-7030 Trondheim, Norway.
| | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, N-1432 Ås, Norway
| | - Ola Storrø
- Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, N-7030 Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, N-7030 Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, N-1432 Ås, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, N-7030 Trondheim, Norway
| |
Collapse
|
13
|
Schei K, Avershina E, Øien T, Rudi K, Follestad T, Salamati S, Ødegård RA. Early gut mycobiota and mother-offspring transfer. Microbiome 2017; 5:107. [PMID: 28837002 PMCID: PMC5571498 DOI: 10.1186/s40168-017-0319-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/28/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND The fungi in the gastrointestinal tract, the gut mycobiota, are now recognised as a significant part of the gut microbiota, and they may be important to human health. In contrast to the adult gut mycobiota, the establishment of the early gut mycobiota has never been described, and there is little knowledge about the fungal transfer from mother to offspring. METHODS In a prospective cohort, we followed 298 pairs of healthy mothers and offspring from 36 weeks of gestation until 2 years of age (1516 samples) and explored the gut mycobiota in maternal and offspring samples. Half of the pregnant mothers were randomised into drinking probiotic milk during and after pregnancy. The probiotic bacteria included Lactobacillus rhamnosus GG (LGG), Bifidobacterium animalis subsp. lactis Bb-12 and Lactobacillus acidophilus La-5. We quantified the fungal abundance of all the samples using qPCR of the fungal internal transcribed spacer (ITS)1 segment, and we sequenced the 18S rRNA gene ITS1 region of 90 high-quantity samples using the MiSeq platform (Illumina). RESULTS The gut mycobiota was detected in most of the mothers and the majority of the offspring. The offspring showed increased odds of having detectable faecal fungal DNA if the mother had detectable fungal DNA as well (OR = 1.54, p = 0.04). The fungal alpha diversity in the offspring gut increased from its lowest at 10 days after birth, which was the earliest sampling point. The fungal diversity and fungal species showed a succession towards the maternal mycobiota as the child aged, with Debaryomyces hansenii being the most abundant species during breast-feeding and Saccharomyces cerevisiae as the most abundant after weaning. Probiotic consumption increased the gut mycobiota abundance in pregnant mothers (p = 0.01). CONCLUSION This study provides the first insight into the early fungal establishment and the succession of fungal species in the gut mycobiota. The results support the idea that the fungal host phenotype is transferred from mother to offspring. TRIAL REGISTRATION Clinicaltrials.gov NCT00159523.
Collapse
Affiliation(s)
- Kasper Schei
- Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine and Health Sciences, NTNU – Norwegian University of Science and Technology, Postboks 8905, 7491 Trondheim, Norway
| | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, NMBU – Norway University of Life Sciences, Ås, Norway
| | - Torbjørn Øien
- Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, NMBU – Norway University of Life Sciences, Ås, Norway
| | - Turid Follestad
- Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU – Norwegian University of Science and Technology, Trondheim, Norway
| | - Saideh Salamati
- ObeCe – Regional Centre for Obesity Research and Innovation, St. Olav’s University Hospital, Trondheim, Norway
| | - Rønnaug Astri Ødegård
- Department of Laboratory Medicine, Children’s and Women’s Health, Faculty of Medicine and Health Sciences, NTNU – Norwegian University of Science and Technology, Postboks 8905, 7491 Trondheim, Norway
- ObeCe – Regional Centre for Obesity Research and Innovation, St. Olav’s University Hospital, Trondheim, Norway
| |
Collapse
|
14
|
Avershina E, Cabrera Rubio R, Lundgård K, Perez Martinez G, Collado MC, Storrø O, Øien T, Dotterud CK, Johnsen R, Rudi K. Effect of probiotics in prevention of atopic dermatitis is dependent on the intrinsic microbiota at early infancy. J Allergy Clin Immunol 2017; 139:1399-1402.e8. [DOI: 10.1016/j.jaci.2016.09.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 08/25/2016] [Accepted: 09/17/2016] [Indexed: 12/26/2022]
|
15
|
Kristoffersen C, Jensen RB, Avershina E, Austbø D, Tauson AH, Rudi K. Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota. Microbes Environ 2016; 31:378-386. [PMID: 27773914 PMCID: PMC5158109 DOI: 10.1264/jsme2.me16061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Knowledge on dynamic interactions in microbiota is pivotal for understanding the role of bacteria in the gut. We herein present comprehensive dynamic models of the horse cecal microbiota, which include short-chained fatty acids, carbohydrate metabolic networks, and taxonomy. Dynamic models were derived from time-series data in a crossover experiment in which four cecum-cannulated horses were fed a starch-rich diet of hay supplemented with barley (starch intake 2 g kg−1 body weight per day) and a fiber-rich diet of only hay. Cecal contents were sampled via the cannula each h for 24 h for both diets. We observed marked differences in the microbial dynamic interaction patterns for Fibrobacter succinogenes, Lachnospiraceae, Streptococcus, Treponema, Anaerostipes, and Anaerovibrio between the two diet groups. Fluctuations and microbiota interactions were the most pronounced for the starch rich diet, with Streptococcus spp. and Anaerovibrio spp. showing the largest fluctuations. Shotgun metagenome sequencing revealed that diet differences may be explained by modular switches in metabolic cross-feeding between microbial consortia in which fermentation is linked to sugar alcohols and amino sugars for the starch-rich diet and monosaccharides for the fiber-rich diet. In conclusion, diet may not only affect the composition of the cecal microbiota, but also dynamic interactions and metabolic cross-feeding.
Collapse
Affiliation(s)
- Camilla Kristoffersen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences
| | | | | | | | | | | |
Collapse
|
16
|
Avershina E, Lundgård K, Sekelja M, Dotterud C, Storrø O, Øien T, Johnsen R, Rudi K. Transition from infant- to adult-like gut microbiota. Environ Microbiol 2016; 18:2226-36. [PMID: 26913851 DOI: 10.1111/1462-2920.13248] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/12/2022]
Abstract
Transition from an infant to an adult associated gut microbiota with age through establishment of strict anaerobic bacteria remains one of the key unresolved questions in gut microbial ecology. Here a comprehensive comparative analysis of stool microbiota in a large cohort of mothers and their children sampled longitudinally up until 2 years of age using sequencing analysis tool was presented that allows realistic microbial diversity estimates. In this work, evidence for the switch from children to adult associated microbial profile between 1 and 2 years of age was provided, suggestively driven by Bifidobacterium breve. An Operational Taxonomic Unit (OTU) belonging to B. breve was highly prevalent in the population throughout the first year of life, and was negatively associated with detection of a range of adult-like OTUs. Although an adult profile was not fully established by 2 years of age, it was demonstrated that with regards to the most prevalent OTUs, their prevalence in the child population by then already resembled that of the adult population. Taken together, it was proposed that late-colonizing OTUs were recruited at a later stage and were not acquired at birth with the recruitment being controlled by gatekeeping OTUs until the age of 1 year.
Collapse
Affiliation(s)
- E Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - K Lundgård
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | - M Sekelja
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway.,Genetic Analysis AS, 0401, Oslo, Norway
| | - C Dotterud
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Department of Dermatology, St. Olavs Hospital, 7006, Trondheim, Norway
| | - O Storrø
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - T Øien
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - R Johnsen
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - K Rudi
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| |
Collapse
|
17
|
Avershina E, Ravi A, Storrø O, Øien T, Johnsen R, Rudi K. Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children. Microbiome 2015; 3:65. [PMID: 26687338 PMCID: PMC4685603 DOI: 10.1186/s40168-015-0125-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/29/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investigated the associations between washing and vacuum cleaning frequency and the gut microbiota composition in a large longitudinal cohort of mothers and their children. The gut microbiota composition was determined using 16S ribosomal RNA (rRNA) gene Illumina deep sequencing. RESULTS We found that high vacuum cleaning frequency about twice or more a week was associated with an altered gut microbiota composition both during pregnancy and for 2-year-old children, while there were no associations with house washing frequency. In total, six Operational Taxonomic Units (OTUs) showed significant False Discovery Rate (FDR) corrected associations with vacuum cleaning frequency for mothers (two positive and four negative) and five for 2-year-old children (four positive and one negative). For mothers and the 2-year-old children, OTUs among the dominant microbiota (average >5 %) showed correlation to vacuum cleaning frequency, with an increase in Faecalibacterium prausnitzii for mothers (p = 0.013, FDR corrected), and Blautia sp. for 2-year children (p = 0.012, FDR corrected). CONCLUSIONS Bacteria showing significant associations are among the dominant gut microbiota, which may indicate indirect immunomodulation of the gut microbiota possibly through increased allergen (dust mites) exposure as a potential mechanism. However, further exploration is needed to unveil mechanistic details.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Ås, Norway.
| | - Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Ås, Norway.
| | - Ola Storrø
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491, Trondheim, Norway.
| | - Torbjørn Øien
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491, Trondheim, Norway.
| | - Roar Johnsen
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491, Trondheim, Norway.
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Ås, Norway.
| |
Collapse
|
18
|
Ravi A, Avershina E, Foley SL, Ludvigsen J, Storrø O, Øien T, Johnsen R, McCartney AL, L’Abée-Lund TM, Rudi K. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Sci Rep 2015; 5:15317. [PMID: 26507767 PMCID: PMC4623605 DOI: 10.1038/srep15317] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/21/2015] [Indexed: 02/08/2023] Open
Abstract
Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.
Collapse
Affiliation(s)
- Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Ekaterina Avershina
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Steven L. Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, Division of Microbiology, Jefferson, AR 72079
| | - Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Ola Storrø
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Torbjørn Øien
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Anne L. McCartney
- Microbial Ecology & Health Group, Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Trine M. L’Abée-Lund
- Norwegian University of Life Sciences, Department of Food safety and Infection Biology, Campus Adamstuen, Oslo 0454, Norway
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| |
Collapse
|
19
|
Abstract
A key message from a range of high profile next generation sequencing studies on the human microbiota is that it composes a tremendously rich community of more than 1000 species within each one of us. Although more recent studies have shown estimates of between 100 and 200 species per individual, this has not yet been made clear in the literature. Currently, the most widely accepted estimate of species richness is therefore five to ten times too high. Here, we will review the different estimates of species richness in the literature, address potential sources of artefacts, the reluctance to correct these, and provide suggestions for future directions.
Collapse
Affiliation(s)
- E. Avershina
- Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, 1430 Ås, Norway
| | - K. Rudi
- Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, 1430 Ås, Norway
| |
Collapse
|
20
|
Ludvigsen J, Rangberg A, Avershina E, Sekelja M, Kreibich C, Amdam G, Rudi K. Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season. Microbes Environ 2015; 30:235-44. [PMID: 26330094 PMCID: PMC4567562 DOI: 10.1264/jsme2.me15019] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Honey bees (Apis mellifera) are prominent crop pollinators and are, thus, important for effective food production. The honey bee gut microbiota is mainly host specific, with only a few species being shared with other insects. It currently remains unclear how environmental/dietary conditions affect the microbiota within a honey bee population over time. Therefore, the aim of the present study was to characterize the composition of the midgut/pyloric microbiota of a honey bee apiary throughout a season. The rationale for investigating the midgut/pyloric microbiota is its dynamic nature. Monthly sampling of a demographic homogenous population of bees was performed between May and October, with concordant recording of the honey bee diet. Mixed Sanger-and Illumina 16S rRNA gene sequencing in combination with a quantitative PCR analysis were used to determine the bacterial composition. A marked increase in α-diversity was detected between May and June. Furthermore, we found that four distinct phylotypes belonging to the Proteobacteria dominated the microbiota, and these displayed major shifts throughout the season. Gilliamella apicola dominated the composition early on, and Snodgrassella alvi began to dominate when the other bacteria declined to an absolute low in October. In vitro co-culturing revealed that G. apicola suppressed S. alvi. No shift was detected in the composition of the microbiota under stable environment/dietary conditions between November and February. Therefore, environmental/dietary changes may trigger the shifts observed in the honey bee midgut/pyloric microbiota throughout a season.
Collapse
Affiliation(s)
- Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department
| | | | | | | | | | | | | |
Collapse
|
21
|
Hansen NCK, Avershina E, Mydland LT, Næsset JA, Austbø D, Moen B, Måge I, Rudi K. High nutrient availability reduces the diversity and stability of the equine caecal microbiota. Microb Ecol Health Dis 2015; 26:27216. [PMID: 26246403 PMCID: PMC4526772 DOI: 10.3402/mehd.v26.27216] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 06/18/2015] [Accepted: 07/03/2015] [Indexed: 11/14/2022]
Abstract
BACKGROUND It is well known that nutrient availability can alter the gut microbiota composition, while the effect on diversity and temporal stability remains largely unknown. METHODS Here we address the equine caecal microbiota temporal stability, diversity, and functionality in response to diets with different levels of nutrient availability. Hay (low and slower nutrient availability) versus a mixture of hay and whole oats (high and more rapid nutrient availability) were used as experimental diets. RESULTS We found major effects on the microbiota despite that the caecal pH was far from sub-clinical acidosis. We found that the low nutrient availability diet was associated with a higher level of both diversity and temporal stability of the caecal microbiota than the high nutrient availability diet. These observations concur with general ecological theories, suggesting a stabilising effect of biological diversity and that high nutrient availability has a destabilising effect through reduced diversity. CONCLUSION Nutrient availability does not only change the composition but also the ecology of the caecal microbiota.
Collapse
Affiliation(s)
- Naja C K Hansen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Liv T Mydland
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Jon A Næsset
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Dag Austbø
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Birgitte Moen
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Aas, Norway
| | - Ingrid Måge
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Aas, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway;
| |
Collapse
|
22
|
Schanche M, Avershina E, Dotterud C, Øien T, Storrø O, Johnsen R, Rudi K. High-Resolution Analyses of Overlap in the Microbiota Between Mothers and Their Children. Curr Microbiol 2015; 71:283-90. [PMID: 26044992 DOI: 10.1007/s00284-015-0843-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/18/2015] [Indexed: 12/01/2022]
Abstract
Understanding the transmission of the human microbiota from mother to child is of major importance. Although we are gaining knowledge using 16S rRNA gene analyses, the resolution of this gene is not sufficient to determine transmission patterns. We therefore developed an Illumina deep sequencing approach targeting the 16-23S rRNA Internal Transcribed Spacer (ITS) for high-resolution microbiota analyses. Using this approach, we analyzed the composition and potential mother to child transmission patterns of the microbiota (milk and stool) in a longitudinal cohort of 20 mother/child pairs. Our results show overlap in the infant stool microbiota with both mother's milk and stool, and that the overlap with stool increases with age. We found an Operational Taxonomic Unit resembling Streptococcus gordonii as the most widespread colonizer of both mothers and their children. In conclusion, the increased resolution of 16-23S rRNA ITS deep sequencing revealed new knowledge about potential transmission patterns of human-associated bacteria.
Collapse
Affiliation(s)
- Melissa Schanche
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | | | | | | | | | | | | |
Collapse
|
23
|
Rodríguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, Avershina E, Rudi K, Narbad A, Jenmalm MC, Marchesi JR, Collado MC. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis 2015; 26:26050. [PMID: 25651996 PMCID: PMC4315782 DOI: 10.3402/mehd.v26.26050] [Citation(s) in RCA: 521] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota has become a relevant aspect of human health. Microbial colonization runs in parallel with immune system maturation and plays a role in intestinal physiology and regulation. Increasing evidence on early microbial contact suggest that human intestinal microbiota is seeded before birth. Maternal microbiota forms the first microbial inoculum, and from birth, the microbial diversity increases and converges toward an adult-like microbiota by the end of the first 3-5 years of life. Perinatal factors such as mode of delivery, diet, genetics, and intestinal mucin glycosylation all contribute to influence microbial colonization. Once established, the composition of the gut microbiota is relatively stable throughout adult life, but can be altered as a result of bacterial infections, antibiotic treatment, lifestyle, surgical, and a long-term change in diet. Shifts in this complex microbial system have been reported to increase the risk of disease. Therefore, an adequate establishment of microbiota and its maintenance throughout life would reduce the risk of disease in early and late life. This review discusses recent studies on the early colonization and factors influencing this process which impact on health.
Collapse
Affiliation(s)
- Juan Miguel Rodríguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Kiera Murphy
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
| | - Catherine Stanton
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
| | - R Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Teagasc Moorepark Food Research Centre, Fermoy, Ireland
| | - Olivia I Kober
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Aas, Norway
| | - Arjan Narbad
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Maria C Jenmalm
- Department of Clinical and Experimental Medicine, Unit of Autoimmunity and Immune Regulation, Division of Clinical Immunology, Linköping University, Linköping, Sweden
| | - Julian R Marchesi
- School of Biosciences, Cardiff University, Cardiff, UK
- Centre for Digestive and Gut Health, Imperial College London, London, UK
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain;
| |
Collapse
|
24
|
Naseribafrouei A, Hestad K, Avershina E, Sekelja M, Linløkken A, Wilson R, Rudi K. Correlation between the human fecal microbiota and depression. Neurogastroenterol Motil 2014; 26:1155-62. [PMID: 24888394 DOI: 10.1111/nmo.12378] [Citation(s) in RCA: 656] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 05/07/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Depression is a chronic syndrome with a pathogenesis linked to various genetic, biological, and environmental factors. Several links between gut microbiota and depression have been established in animal models. In humans, however, few correlations have yet been demonstrated. The aim of our work was therefore to identify potential correlations between human fecal microbiota (as a proxy for gut microbiota) and depression. METHODS We analyzed fecal samples from 55 people, 37 patients, and 18 non-depressed controls. Our analyses were based on data generated by Illumina deep sequencing of 16S rRNA gene amplicons. KEY RESULTS We found several correlations between depression and fecal microbiota. The correlations, however, showed opposite directions even for closely related Operational Taxonomic Units (OTU's), but were still associated with certain higher order phylogroups. The order Bacteroidales showed an overrepresentation (p = 0.05), while the family Lachnospiraceae showed an underrepresentation (p = 0.02) of OTU's associated with depression. At low taxonomic levels, there was one clade consisting of five OTU's within the genus Oscillibacter, and one clade within Alistipes (consisting of four OTU's) that showed a significant association with depression (p = 0.03 and 0.01, respectively). CONCLUSIONS & INFERENCES The Oscillibacter type strain has valeric acid as its main metabolic end product, a homolog of neurotransmitter GABA, while Alistipes has previously been shown to be associated with induced stress in mice. In conclusion, the taxonomic correlations detected here may therefore correspond to mechanistic models.
Collapse
Affiliation(s)
- A Naseribafrouei
- Faculty of Education and Science, Hedmark University College, Hamar, Norway
| | | | | | | | | | | | | |
Collapse
|
25
|
Ravi A, Avershina E, Ludvigsen J, L'Abée-Lund TM, Rudi K. Integrons in the intestinal microbiota as reservoirs for transmission of antibiotic resistance genes. Pathogens 2014; 3:238-48. [PMID: 25437798 PMCID: PMC4243444 DOI: 10.3390/pathogens3020238] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 12/13/2022] Open
Abstract
The human intestinal microbiota plays a major beneficial role in immune development and resistance to pathogens. The use of antibiotics, however, can cause the spread of antibiotic resistance genes within the resident intestinal microbiota. Important vectors for this are integrons. This review therefore focuses on the integrons in non-pathogenic bacteria as a potential source for the development and persistence of multidrug resistance. Integrons are a group of genetic elements which are assembly platforms that can capture specific gene cassettes and express them. Integrons in pathogenic bacteria have been extensively investigated, while integrons in the intestinal microbiota have not yet gained much attention. Knowledge of the integrons residing in the microbiota, however, can potentially aid in controlling the spread of antibiotic resistance genes to pathogens.
Collapse
Affiliation(s)
- Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Ekaterina Avershina
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Trine M L'Abée-Lund
- Norwegian University of Life Sciences, Department of Food Safety and Infection Biology, Campus Adamstuen, Oslo 0454, Norway.
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| |
Collapse
|
26
|
Abstract
The current leading view is that functionality and not phylotype is the most important determinant for the services provided by the gut microbiota. Here we present an alternative opinion, advocating the importance of phylotype in addition to function. We believe the literature is misled by technical artifacts in defining operational taxonomic units (OTUs), which are binned groups of bacteria based on sequence homology. Furthermore, the current metagenomic approaches where the total DNA in a sample is mixed prior to sequencing and subsequently resolved by a bioinformatics approach, are highly error prone with respect to both functional and phylotype assignments. We argue that the directions of the OTU and metagenome errors are such that stable phylotypes are overlooked, while functional stability is overestimated. Taking these errors into account, we propose that phylotype represents an interface for functionality, and is for this reason an important determinant for the services provided by the gut microbiota to the host.
Collapse
Affiliation(s)
- E Avershina
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Universitetstunet 3, 1432 Ås, Norway
| | | |
Collapse
|
27
|
Avershina E, Storrø O, Øien T, Johnsen R, Pope P, Rudi K. Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol Ecol 2013; 87:280-90. [PMID: 24112053 DOI: 10.1111/1574-6941.12223] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/13/2013] [Accepted: 09/13/2013] [Indexed: 01/22/2023] Open
Abstract
Despite the importance, the diversity of the human infant gut microbiota still remains poorly characterized at the regional scale. Here, we investigated the faecal microbiota diversity in a large 16S rRNA gene data set from a healthy cohort of 86 mothers and their children from the Trondheim region in Norway. Samples were collected from mothers during early and late pregnancy, as well as from their children at 3 days, 10 days, 4 months, 1 year and 2 years of age. Using a combination of Sanger sequencing of amplicon mixtures (without cloning), real-time quantitative PCR and deep pyrosequencing, we observed a clear age-related colonization pattern in children that was surprisingly evident between 3- and 10-day samples. In contrast, we did not observe any shifts in microbial composition during pregnancy. We found that alpha-diversity was highest at 2 years and lowest at 4 months, whereas beta-diversity estimates indicated highest interindividual variation in newborns. Variation significantly decreased by the age of 10 days and was observed to be convergent over time; however, there were still major differences between 2 years and adults whom exhibited the lowest interindividual diversity. Taken together, the major age-affiliated population shift within gut microbiota suggests that there are important mechanisms for transmission and persistence of gut bacteria that remain unknown.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, University of Life Sciences, Ås, Norway
| | | | | | | | | | | |
Collapse
|
28
|
Avershina E, Frisli T, Rudi K. De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data. Microbes Environ 2013; 28:211-6. [PMID: 23603801 PMCID: PMC4070667 DOI: 10.1264/jsme2.me12157] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We addressed the challenges of analyzing next-generation 16S rRNA gene deep sequencing data from the uncharacterized microbial majority. This was performed using a novel de novo semi-alignment approach. The semi-alignments were based on Orthologous Tri-Nucleotides (OTNs), which are identical trinucleotides located in the same sequence region. OTNs in high error homopolymeric tracts were excluded to avoid overestimation of genetic distances. Phylogenetic information was derived assuming an exponential decay in shared OTNs between pairs of bacteria. OTN relatedness was also explored through principal component analysis (PCA). In evaluating the OTN approach we reanalyzed a dataset consisting of triplicate GS FLX titanium pyrosequencing runs for each of two experimental soil samples, in addition to analyses of the Greengenes core dataset. The conclusion from these comparisons was that the OTN approach was superior to traditional alignments both with respect to speed and accuracy. We therefore believe that our OTN-based semi-alignment approach will be a valuable contribution to future exploration of deep sequencing data.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | | | | |
Collapse
|
29
|
Nwosu FC, Thorkildsen LT, Avershina E, Ricanek P, Perminow G, Brackmann S, Vatn MH, Rudi K. Age-dependent fecal bacterial correlation to inflammatory bowel disease for newly diagnosed untreated children. Gastroenterol Res Pract 2013; 2013:302398. [PMID: 23690761 PMCID: PMC3652150 DOI: 10.1155/2013/302398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 04/01/2013] [Indexed: 12/22/2022] Open
Abstract
The knowledge about correlation patterns between the fecal microbiota and inflammatory bowel diseases (IBD)-comprising the two subforms Crohn's disease (CD) and ulcerative colitis (UC)-for newly diagnosed untreated children is limited. To address this knowledge gap, a selection of faecal specimens (CD, n = 27 and UC, n = 16) and non-IBD controls (n = 30) children (age < 18 years) was analysed utilising bacterial small subunit (SSU) rRNA. We found, surprising age dependence for the fecal microbiota correlating to IBD. The most pronounced patterns were that E. coli was positively (R (2) = 0.16, P = 0.05) and Bacteroidetes, negatively (R (2) = 0.15, P = 0.05) correlated to age for CD patients. For UC, we found an apparent opposite age-related disease correlation for both Bacteroides and Escherichia. In addition, there was an overrepresentation of Haemophilus for the UC children. From our, results we propose a model where the aetiology of IBD is related to an on-going immunological development in children requiring different age-dependent bacterial stimuli. The impact of our findings could be a better age stratification for understanding and treating IBD in children.
Collapse
Affiliation(s)
- Felix Chinweije Nwosu
- Hedmark University College, Hamar, Norway
- Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, Ås, Oslo, Norway
| | | | - Ekaterina Avershina
- Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, Ås, Oslo, Norway
| | - Petr Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- EpiGen Institute, Research Centre, Akershus University Hospital, Lørenskog, Norway
| | - Gøri Perminow
- Pediatric Department, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Stephan Brackmann
- EpiGen Institute, Akershus University Hospital, University of Oslo, Oslo, Norway
| | - Morten H. Vatn
- EpiGen Institute, Akershus University Hospital, University of Oslo, Oslo, Norway
- Medical Clinic, Oslo University Hospital, Rikshospitalet, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Science, Norwegian University for Life Sciences, Ås, Oslo, Norway
| |
Collapse
|