1
|
Jatkowska A, Gkikas K, Nichols B, Short B, Rizou VK, Kapranos P, Gunnewiek JK, Christina E, Svolos V, Quince C, Gerasimidis K. Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clin Nutr 2024; 43:1200-1207. [PMID: 38615449 DOI: 10.1016/j.clnu.2024.04.010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/20/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
INTRODUCTION Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact of varying doses of EN on the gut microbiome remains understudied. METHODS Healthy adults replaced all (100% EN) or part (85% EN, 50% EN and 20% EN) of their energy requirements with EN for 7 days. Faecal samples were collected before and on day 7 of interventions. Faecal pH, short chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and 16S rRNA sequencing were performed. Dietary assessment was performed with 7-day food diaries. RESULTS Sixty-one participants (31 females; median (IQR) age: 24.7 (23.0-27.8) years) were recruited. A dose-dependent impact of EN on faecal microbiota, SCFAs, BCFAs) and pH was observed, with changes detectable at EN intakes of at least 50% of energy requirements. 100% and 85% EN reduced the abundance of fibre-fermenting taxa such as Agathobacter, Faecalibaterium, Succinivibrio and Acidaminococcus. In parallel, potentially harmful organisms like Eubacterium, Actinomyces, and Klebsiella increased. In the 50% EN group, adherence to a diet high in fish, vegetables, potatoes, non-alcoholic beverages, and fat spreads, and low in cereal products, milk, and meat negatively correlated with changes in microbiota structure (r = -0.75, P = 0.025). This signal was not observed when using compositional tools for microbiota analysis. CONCLUSIONS EN detrimentally influences the faecal microbiota and diet-related bacterial metabolites in a dose-dependent manner, particularly at doses of at least 50%. The findings of this study have implications for the dietary management and counselling of patients receiving high volume EN.
Collapse
Affiliation(s)
- Aleksandra Jatkowska
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - Konstantinos Gkikas
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - Ben Nichols
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - Bryn Short
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | | | - Panagiotis Kapranos
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | | | - Edelyn Christina
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - Vaios Svolos
- Human Nutrition, School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | | | | |
Collapse
|
2
|
Nichols B, Briola A, Logan M, Havlik J, Mascellani A, Gkikas K, Milling S, Ijaz UZ, Quince C, Svolos V, Russell RK, Hansen R, Gerasimidis K. Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn's disease. Am J Clin Nutr 2024; 119:885-895. [PMID: 38569785 PMCID: PMC11007740 DOI: 10.1016/j.ajcnut.2023.12.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Predicting response to exclusive enteral nutrition (EEN) in active Crohn's disease (CD) could lead to therapy personalization and pretreatment optimization. OBJECTIVES This study aimed to explore the ability of pretreatment parameters to predict fecal calprotectin (FCal) levels at EEN completion in a prospective study in children with CD. METHODS In children with active CD, clinical parameters, dietary intake, cytokines, inflammation-related blood proteomics, and diet-related metabolites, metabolomics and microbiota in feces, were measured before initiation of 8 wk of EEN. Prediction of FCal levels at EEN completion was performed using machine learning. Data are presented with medians (IQR). RESULTS Of 37 patients recruited, 15 responded (FCal < 250 μg/g) to EEN (responders) and 22 did not (nonresponders). Clinical and immunological parameters were not associated with response to EEN. Responders had lesser (μmol/g) butyrate [responders: 13.2 (8.63-18.4) compared with nonresponders: 22.3 (12.0-32.0); P = 0.03], acetate [responders: 49.9 (46.4-68.4) compared with nonresponders: 70.4 (57.0-95.5); P = 0.027], phenylacetate [responders: 0.175 (0.013-0.611) compared with nonresponders: 0.943 (0.438-1.35); P = 0.021], and a higher microbiota richness [315 (269-347) compared with nonresponders: 243 (205-297); P = 0.015] in feces than nonresponders. Responders consumed (portions/1000 kcal/d) more confectionery products [responders: 0.55 (0.38-0.72) compared with nonresponders: 0.19 (0.01-0.38); P = 0.045]. A multicomponent model using fecal parameters, dietary data, and clinical and immunological parameters predicted response to EEN with 78% accuracy (sensitivity: 80%; specificity: 77%; positive predictive value: 71%; negative predictive value: 85%). Higher taxon abundance from Ruminococcaceae, Lachnospiraceae, and Bacteroides and phenylacetate, butyrate, and acetate were the most influential variables in predicting lack of response to EEN. CONCLUSIONS We identify microbial signals and diet-related metabolites in feces, which could comprise targets for pretreatment optimization and personalized nutritional therapy in pediatric CD.
Collapse
Affiliation(s)
- Ben Nichols
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Anny Briola
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Michael Logan
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Jaroslav Havlik
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Anna Mascellani
- Department of Food Science, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Konstantinos Gkikas
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Simon Milling
- School of Infection and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Umer Zeeshan Ijaz
- Civil Engineering, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | | | - Vaios Svolos
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children and Young People, Edinburgh, United Kingdom
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom; Department of Child Health, Division of Clinical and Molecular Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom.
| |
Collapse
|
3
|
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol 2024:10.1038/s41587-023-01983-6. [PMID: 38168989 DOI: 10.1038/s41587-023-01983-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/08/2023] [Indexed: 01/05/2024]
Abstract
We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.
Collapse
Affiliation(s)
- Gaëtan Benoit
- Organisms and Ecosystems, Earlham Institute, Norwich, UK
| | | | - Robert James
- Gut Microbes and Health, Quadram Institute, Norwich, UK
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, UK.
- School of Biological Sciences, University of East Anglia, Norwich, UK.
- Warwick Medical School, University of Warwick, Coventry, UK.
| |
Collapse
|
4
|
Vos M, Padfield D, Quince C, Vos R. Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol 2023; 99:fiad154. [PMID: 37996397 PMCID: PMC10710302 DOI: 10.1093/femsec/fiad154] [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: 09/13/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.
Collapse
Affiliation(s)
- Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
- Environment and Sustainability Institute, University of Exeter, Treliever Road, Penryn Campus, Penryn, TR10 9FE, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Rutger Vos
- Naturalis Biodiversity Center, Understanding Evolution, Darwinweg 2, Leiden 2333 CR, the Netherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, the Netherlands
| |
Collapse
|
5
|
Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 2023; 31:1111-1125.e6. [PMID: 37339626 DOI: 10.1016/j.chom.2023.05.024] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
Collapse
Affiliation(s)
- Clémence Frioux
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK; Inria, University of Bordeaux, INRAE, 33400 Talence, France.
| | - Rebecca Ansorge
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Ezgi Özkurt
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | | | - Joachim Fritscher
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Christopher Quince
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo 0318, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA 94148, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Falk Hildebrand
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK.
| |
Collapse
|
6
|
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs. bioRxiv 2023:2023.07.07.548136. [PMID: 37786716 PMCID: PMC10541625 DOI: 10.1101/2023.07.07.548136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-k' approach for dealing with variations in genome coverage depth and an abundance-based filtering strategy for simplifying strain complexity. The resulting algorithm is more efficient than the state-of-the-art but with better assembly results. metaMDBG was 1.5 to 12 times faster than competing assemblers and requires between one-tenth and one-thirtieth of the memory across a range of data sets. We obtained up to twice as many high-quality circularised prokaryotic metagenome assembled genomes (MAGs) on the most complex communities, and a better recovery of viruses and plasmids. metaMDBG performs particularly well for abundant organisms whilst being robust to the presence of strain diversity. The result is that for the first time it is possible to efficiently reconstruct the majority of complex communities by abundance as near-complete MAGs.
Collapse
Affiliation(s)
- Gaëtan Benoit
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
| | | | - Robert James
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Adam M. Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| |
Collapse
|
7
|
Shaw DG, Aguirre-Gamboa R, Vieira MC, Gona S, DiNardi N, Wang A, Dumaine A, Gelderloos-Arends J, Earley ZM, Meckel KR, Ciszewski C, Castillo A, Monroe K, Torres J, Shah SC, Colombel JF, Itzkowitz S, Newberry R, Cohen RD, Rubin DT, Quince C, Cobey S, Jonkers IH, Weber CR, Pekow J, Wilson PC, Barreiro LB, Jabri B. Antigen-driven colonic inflammation is associated with development of dysplasia in primary sclerosing cholangitis. Nat Med 2023; 29:1520-1529. [PMID: 37322120 PMCID: PMC10287559 DOI: 10.1038/s41591-023-02372-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 05/26/2022] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
Primary sclerosing cholangitis (PSC) is an immune-mediated disease of the bile ducts that co-occurs with inflammatory bowel disease (IBD) in almost 90% of cases. Colorectal cancer is a major complication of patients with PSC and IBD, and these patients are at a much greater risk compared to patients with IBD without concomitant PSC. Combining flow cytometry, bulk and single-cell transcriptomics, and T and B cell receptor repertoire analysis of right colon tissue from 65 patients with PSC, 108 patients with IBD and 48 healthy individuals we identified a unique adaptive inflammatory transcriptional signature associated with greater risk and shorter time to dysplasia in patients with PSC. This inflammatory signature is characterized by antigen-driven interleukin-17A (IL-17A)+ forkhead box P3 (FOXP3)+ CD4 T cells that express a pathogenic IL-17 signature, as well as an expansion of IgG-secreting plasma cells. These results suggest that the mechanisms that drive the emergence of dysplasia in PSC and IBD are distinct and provide molecular insights that could guide prevention of colorectal cancer in individuals with PSC.
Collapse
Affiliation(s)
- Dustin G Shaw
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Raúl Aguirre-Gamboa
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Marcos C Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Saideep Gona
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Nicholas DiNardi
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anni Wang
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne Dumaine
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jody Gelderloos-Arends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zachary M Earley
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Cezary Ciszewski
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anabella Castillo
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly Monroe
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Joana Torres
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
- Division of Gastroenterology, Hospital Luz, Lisboa, Portugal
- Faculty of Medicine, Universidade de Lisboa, Lisboa, Portugal
| | - Shailja C Shah
- Division of Gastroenterology, University of California San Diego, San Diego, CA, USA
- Jennifer Moreno VA San Diego Healthcare System, San Diego, CA, USA
| | - Jean-Frédéric Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Itzkowitz
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rodney Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Russell D Cohen
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - David T Rubin
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Iris H Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Joel Pekow
- University of Chicago Inflammatory Bowel Disease Center, Chicago, IL, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Department of Medicine, University of Chicago, Chicago, IL, USA
- Section of Rheumatology, University of Chicago, Chicago, IL, USA
| | - Luis B Barreiro
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL, USA.
- Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Pathology, University of Chicago, Chicago, IL, USA.
- Department of Pediatrics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
8
|
Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biol 2023; 24:78. [PMID: 37069665 PMCID: PMC10108530 DOI: 10.1186/s13059-023-02924-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 07/03/2022] [Accepted: 04/07/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. RESULTS Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. CONCLUSIONS These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
Collapse
Affiliation(s)
- Andrea R Watson
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Marisela Silva
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Alon Shaiber
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Emily Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph M Runde
- Department of Pediatrics, Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA
| | - Sonny T M Lee
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dina Kao
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - David T Rubin
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Thomas Louie
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany.
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA.
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany.
| |
Collapse
|
9
|
Runde J, Veseli I, Fogarty EC, Watson AR, Clayssen Q, Yosef M, Shaiber A, Verma R, Quince C, Gerasimidis K, Rubin DT, Eren AM. Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease. J Crohns Colitis 2023:7080705. [PMID: 36934439 DOI: 10.1093/ecco-jcc/jjad031] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Indexed: 03/20/2023]
Abstract
BACKGROUND AND AIMS Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking. METHODS Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis. RESULTS Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy. CONCLUSIONS These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.
Collapse
Affiliation(s)
- Joseph Runde
- Department of Pediatrics, Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL 60637, USA
| | - Emily C Fogarty
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Andrea R Watson
- Committee on Microbiology, The University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Quentin Clayssen
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Mahmoud Yosef
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Alon Shaiber
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ritu Verma
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
| | | | | | - David T Rubin
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany.,Alfred-Wegener-Institute for Marine and Polar Research, 27570 Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
| |
Collapse
|
10
|
Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
Collapse
Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
| |
Collapse
|
11
|
Pinhassi J, Farnelid H, García SM, Teira E, Galand PE, Obernosterer I, Quince C, Vila-Costa M, Gasol JM, Lundin D, Andersson AF, Labrenz M, Riemann L. Functional responses of key marine bacteria to environmental change – toward genetic counselling for coastal waters. Front Microbiol 2022; 13:869093. [DOI: 10.3389/fmicb.2022.869093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Coastal ecosystems deteriorate globally due to human-induced stress factors, like nutrient loading and pollution. Bacteria are critical to marine ecosystems, e.g., by regulating nutrient cycles, synthesizing vitamins, or degrading pollutants, thereby providing essential ecosystem services ultimately affecting economic activities. Yet, until now bacteria are overlooked both as mediators and indicators of ecosystem health, mainly due to methodological limitations in assessing bacterial ecosystem functions. However, these limitations are largely overcome by the advances in molecular biology and bioinformatics methods for characterizing the genetics that underlie functional traits of key bacterial populations – “key” in providing important ecosystem services, being abundant, or by possessing high metabolic rates. It is therefore timely to analyze and define the functional responses of bacteria to human-induced effects on coastal ecosystem health. We posit that categorizing the responses of key marine bacterial populations to changes in environmental conditions through modern microbial oceanography methods will allow establishing the nascent field of genetic counselling for our coastal waters. This requires systematic field studies of linkages between functional traits of key bacterial populations and their ecosystem functions in coastal seas, complemented with systematic experimental analyses of the responses to different stressors. Research and training in environmental management along with dissemination of results and dialogue with societal actors are equally important to ensure the role of bacteria is understood as fundamentally important for coastal ecosystems. Using the responses of microorganisms as a tool to develop genetic counselling for coastal ecosystems can ultimately allow for integrating bacteria as indicators of environmental change.
Collapse
|
12
|
Muscatt G, Hilton S, Raguideau S, Teakle G, Lidbury IDEA, Wellington EMH, Quince C, Millard A, Bending GD, Jameson E. Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere. Microbiome 2022; 10:181. [PMID: 36280853 PMCID: PMC9590211 DOI: 10.1186/s40168-022-01371-3] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/18/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions. RESULTS Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation. CONCLUSIONS Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.
Collapse
Affiliation(s)
- George Muscatt
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sally Hilton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Sebastien Raguideau
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Graham Teakle
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Coventry, UK
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | - Christopher Quince
- School of Life Sciences, University of Warwick, Coventry, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Andrew Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK.
- School of Natural Sciences, Bangor University, Bangor, UK.
| |
Collapse
|
13
|
Ijaz UZ, Gundogdu O, Keating C, van Eekert M, Gibson W, Parkhill J, Abilahi F, Liseki B, Nguyen VA, Sudgen S, Quince C, Ensink JHJ, Torondel B, Walker AW. Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate. Front Microbiol 2022; 13:960747. [PMID: 36212864 PMCID: PMC9539666 DOI: 10.3389/fmicb.2022.960747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Pit latrines are used by billions of people globally, often in developing countries where they provide a low-tech and low-cost sanitation method. However, health and social problems can arise from a lack of emptying or maintenance of these facilities. A better understanding of the biological and environmental parameters within pit latrines could inform attempts to enhance material decomposition rates, and therefore slow fill-up rate. In this study, we have performed a spatial analysis of 35 Tanzanian pit latrines to identify bacteria and environmental factors that are associated with faster or slower pit latrine fill-up rates. Using ordination of microbial community data, we observed a linear gradient in terms of beta diversity with increasing pit latrine sample depth, corresponding to a shift in microbial community structure from gut-associated families in the top layer to environmental- and wastewater-associated taxa at greater depths. We also investigated the bacteria and environmental parameters associated with fill-up rates, and identified pH, volatile solids, and volatile fatty acids as features strongly positively correlated with pit latrine fill-up rates, whereas phosphate was strongly negatively correlated with fill-up rate. A number of pit latrine microbiota taxa were also correlated with fill-up rates. Using a multivariate regression, we identified the Lactobacillaceae and Incertae_Sedis_XIII taxa as particularly strongly positively and negatively correlated with fill-up rate, respectively. This study therefore increases knowledge of the microbiota within pit latrines, and identifies potentially important bacteria and environmental variables associated with fill-up rates. These new insights may be useful for future studies investigating the decomposition process within pit latrines.
Collapse
Affiliation(s)
- Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
- *Correspondence: Umer Zeeshan Ijaz
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ciara Keating
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | | | - Walter Gibson
- Bear Valley Ventures Ltd., Tarporley, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | | | | | - Steven Sudgen
- Environmental Health Group, Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Jeroen H. J. Ensink
- Environmental Health Group, Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Belen Torondel
- Environmental Health Group, Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alan W. Walker
- Pathogen Genomics, Wellcome Sanger Institute, Hinxton, United Kingdom
- The Rowett Institute, University of Aberdeen, Foresterhill, United Kingdom
| |
Collapse
|
14
|
Bawn M, Hernandez J, Trampari E, Thilliez G, Quince C, Webber MA, Kingsley RA, Hall N, Macaulay IC. Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella. Microb Genom 2022; 8. [PMID: 36125951 DOI: 10.1099/mgen.0.000871] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for in vitro evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of Salmonella in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.
Collapse
Affiliation(s)
- Matt Bawn
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | | | - Gaetan Thilliez
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Christopher Quince
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mark A Webber
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UA, UK
| | - Robert A Kingsley
- Quadram Institute, Norwich Research Park, Norwich, NR4 7UQ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Iain C Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK.,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| |
Collapse
|
15
|
Rees NP, Shaheen W, Quince C, Tselepis C, Horniblow RD, Sharma N, Beggs AD, Iqbal TH, Quraishi MN. Systematic review of donor and recipient predictive biomarkers of response to faecal microbiota transplantation in patients with ulcerative colitis. EBioMedicine 2022; 81:104088. [PMID: 35660786 PMCID: PMC9163485 DOI: 10.1016/j.ebiom.2022.104088] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/14/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Nia Paddison Rees
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, UK
| | - Walaa Shaheen
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, UK
| | | | - Chris Tselepis
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Clinical Sciences, School of Biomedical Sciences, University of Birmingham, UK
| | - Richard D Horniblow
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Clinical Sciences, School of Biomedical Sciences, University of Birmingham, UK
| | - Naveen Sharma
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Andrew D Beggs
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Tariq H Iqbal
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Microbiology and Infection, University of Birmingham, UK
| | - Mohammed Nabil Quraishi
- University of Birmingham Microbiome Treatment Centre, Birmingham, UK; Institute of Cancer and Genomic Sciences, University of Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
| |
Collapse
|
16
|
Borsetto C, Raguideau S, Travis E, Kim DW, Lee DH, Bottrill A, Stark R, Song L, Cha CJ, Pearson J, Quince C, Singer AC, Wellington EMH. Impact of sulfamethoxazole on a riverine microbiome. Water Res 2021; 201:117382. [PMID: 34225233 DOI: 10.1016/j.watres.2021.117382] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.
Collapse
Affiliation(s)
- Chiara Borsetto
- University of Warwick, School of Life Sciences, Coventry, UK.
| | | | - Emma Travis
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
| | - Andrew Bottrill
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Richard Stark
- University of Warwick, School of Life Sciences, Coventry, UK
| | - Lijiang Song
- University of Warwick, Department of Chemistry, Coventry, UK
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, Republic of Korea
| | | | | | | | | |
Collapse
|
17
|
Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE. STRONG: metagenomics strain resolution on assembly graphs. Genome Biol 2021; 22:214. [PMID: 34311761 PMCID: PMC8311964 DOI: 10.1186/s13059-021-02419-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.
Collapse
Affiliation(s)
- Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK.
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, 20892, MD, USA.
| | - Sebastien Raguideau
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Robert James
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | | | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Rayan Chikhi
- Department of Computational Biology, Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France
| | - Aaron E Darling
- The iThree institute, University of Technology Sydney, 15 Broadway, Ultimo, 2007, NSW, Australia
| |
Collapse
|
18
|
Vicedomini R, Quince C, Darling AE, Chikhi R. Strainberry: automated strain separation in low-complexity metagenomes using long reads. Nat Commun 2021; 12:4485. [PMID: 34301928 PMCID: PMC8302730 DOI: 10.1038/s41467-021-24515-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023] Open
Abstract
High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.
Collapse
Affiliation(s)
- Riccardo Vicedomini
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, United Kingdom
- Gut Microbes and Health, Quadram Institute, Norwich, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Aaron E Darling
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France
| |
Collapse
|
19
|
Mahé F, Czech L, Stamatakis A, Quince C, de Vargas C, Dunthorn M, Rognes T. Swarm v3: towards tera-scale amplicon clustering. Bioinformatics 2021; 38:267-269. [PMID: 34244702 PMCID: PMC8696092 DOI: 10.1093/bioinformatics/btab493] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/24/2021] [Accepted: 07/01/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes. RESULTS When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic. AVAILABILITY AND IMPLEMENTATION Source code and binaries are available at https://github.com/torognes/swarm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Lucas Czech
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, UK,Gut Microbes and Health, Quadram Institute, Norwich, UK,Warwick Medical School, University of Warwick, Coventry, UK
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway,Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| |
Collapse
|
20
|
Sheridan PO, Raguideau S, Quince C, Holden J, Zhang L, Williams TA, Gubry-Rangin C. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat Commun 2020; 11:5494. [PMID: 33127895 PMCID: PMC7603488 DOI: 10.1038/s41467-020-19132-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.
Collapse
Affiliation(s)
- Paul O Sheridan
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Christopher Quince
- Warwick Medical School, University of Warwick, Coventry, UK
- Organisms and Ecosystems, Earlham Institute, Norwich, UK
- Gut Microbes and Health, Quadram Institute, Norwich, UK
| | - Jennifer Holden
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Lihong Zhang
- European Centre for Environment and Human Health, Medical School, University of Exeter, Exeter, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | |
Collapse
|
21
|
Trego AC, Galvin E, Sweeney C, Dunning S, Murphy C, Mills S, Nzeteu C, Quince C, Connelly S, Ijaz UZ, Collins G. Growth and Break-Up of Methanogenic Granules Suggests Mechanisms for Biofilm and Community Development. Front Microbiol 2020; 11:1126. [PMID: 32582085 PMCID: PMC7285868 DOI: 10.3389/fmicb.2020.01126] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 01/28/2020] [Accepted: 05/05/2020] [Indexed: 12/14/2022] Open
Abstract
Methanogenic sludge granules are densely packed, small, spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. Each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion (AD) process. Information on exactly how methanogenic granules develop, and their eventual fate will be important for precision management of environmental biotechnologies. Granules from a full-scale bioreactor were size-separated into small (0.6-1 mm), medium (1-1.4 mm), and large (1.4-1.8 mm) size fractions. Twelve laboratory-scale bioreactors were operated using either small, medium, or large granules, or unfractionated sludge. After >50 days of operation, the granule size distribution in each of the small, medium, and large bioreactor sets had diversified beyond-to both bigger and smaller than-the size fraction used for inoculation. Interestingly, extra-small (XS; <0.6 mm) granules were observed, and retained in all of the bioreactors, suggesting the continuous nature of granulation, and/or the breakage of larger granules into XS bits. Moreover, evidence suggested that even granules with small diameters could break. "New" granules from each emerging size were analyzed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae, and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration (MINT) analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules.
Collapse
Affiliation(s)
- Anna Christine Trego
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Evan Galvin
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Conor Sweeney
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sinéad Dunning
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Cillian Murphy
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Simon Mills
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Corine Nzeteu
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | | | - Stephanie Connelly
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Umer Zeeshan Ijaz
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Gavin Collins
- Microbial Communities Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
- Ryan Institute, National University of Ireland Galway, Galway, Ireland
| |
Collapse
|
22
|
Alneberg J, Bennke C, Beier S, Bunse C, Quince C, Ininbergs K, Riemann L, Ekman M, Jürgens K, Labrenz M, Pinhassi J, Andersson AF. Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes. Commun Biol 2020; 3:119. [PMID: 32170201 PMCID: PMC7070063 DOI: 10.1038/s42003-020-0856-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 07/03/2019] [Accepted: 02/25/2020] [Indexed: 11/16/2022] Open
Abstract
The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes’ placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data. Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes.
Collapse
Affiliation(s)
- Johannes Alneberg
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christin Bennke
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | - Sara Beier
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.,CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, Sorbonne Université, Banyuls/mer, France
| | - Carina Bunse
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.,Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | | | - Karolina Ininbergs
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lasse Riemann
- Department of Biology, Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Martin Ekman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research, Warnemünde, Germany
| | | | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus, University, Kalmar, Sweden
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
| |
Collapse
|
23
|
Bubier JA, Philip VM, Quince C, Campbell J, Zhou Y, Vishnivetskaya T, Duvvuru S, Blair RH, Ndukum J, Donohue KD, Foster CM, Mellert DJ, Weinstock G, Culiat CT, O'Hara BF, Palumbo AV, Podar M, Chesler EJ. A Microbe Associated with Sleep Revealed by a Novel Systems Genetic Analysis of the Microbiome in Collaborative Cross Mice. Genetics 2020; 214:719-733. [PMID: 31896565 PMCID: PMC7054020 DOI: 10.1534/genetics.119.303013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/30/2019] [Indexed: 12/20/2022] Open
Abstract
The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.
Collapse
Affiliation(s)
| | - Vivek M Philip
- The Jackson Laboratory, Bar Harbor, Maine 04609
- Genome Science and Technology Program, University of Tennessee, Tennessee 37830
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | | | - James Campbell
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
- Department of Natural Sciences, Northwest Missouri State University, Maryville, Missouri 64468
| | | | - Tatiana Vishnivetskaya
- Genome Science and Technology Program, University of Tennessee, Tennessee 37830
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | - Suman Duvvuru
- Genome Science and Technology Program, University of Tennessee, Tennessee 37830
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | - Rachel Hageman Blair
- Department of Biostatistics, State University of New York at Buffalo, New York, 14260
| | | | - Kevin D Donohue
- Signal Solutions, LLC, Lexington, Kentucky 40506
- Electrical and Computer Engineering Department, University of Kentucky, Lexington, Kentucky 40508
| | - Carmen M Foster
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | | | | | - Cymbeline T Culiat
- Genome Science and Technology Program, University of Tennessee, Tennessee 37830
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | - Bruce F O'Hara
- Signal Solutions, LLC, Lexington, Kentucky 40506
- Department of Biology, University of Kentucky, Lexington, Kentucky 40508
| | - Anthony V Palumbo
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| | - Elissa J Chesler
- The Jackson Laboratory, Bar Harbor, Maine 04609
- Genome Science and Technology Program, University of Tennessee, Tennessee 37830
- Biosciences Division, Oak Ridge National Laboratory, Tennessee 37830
| |
Collapse
|
24
|
Lee K, Kim DW, Lee DH, Kim YS, Bu JH, Cha JH, Thawng CN, Hwang EM, Seong HJ, Sul WJ, Wellington EMH, Quince C, Cha CJ. Mobile resistome of human gut and pathogen drives anthropogenic bloom of antibiotic resistance. Microbiome 2020; 8:2. [PMID: 31910889 PMCID: PMC6947943 DOI: 10.1186/s40168-019-0774-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [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: 09/26/2019] [Accepted: 12/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. RESULTS The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile genetic elements rather than particular gut taxa and mainly responsible for anthropogenically driven bloom of the downstream river resistome. Furthermore, both sequence- and phenotype-based analyses revealed environmental relatives of clinically important proteobacteria as major carriers of these ARGs. CONCLUSIONS Our results demonstrate a more nuanced view of the impact of anthropogenic activities on the river resistome: fecal contamination is present and allows the transmission of ARGs to the environmental resistome, but these mobile genes rather than resistant fecal bacteria proliferate in environmental relatives of their original hosts. Video abstract.
Collapse
Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dae-Wi Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Do-Hoon Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ji-Hye Bu
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Ju-Hee Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Cung Nawl Thawng
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Eun-Mi Hwang
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | | | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| |
Collapse
|
25
|
Quraishi MNN, Yalchin M, Blackwell C, Segal J, Sharma N, Hawkey P, McCune V, Hart AL, Gaya D, Ives NJ, Magill L, Loi S, Hewitt C, Gerasimidis K, Loman NJ, Hansen R, McMullan C, Mathers J, Quince C, Crees N, Iqbal T. STOP-Colitis pilot trial protocol: a prospective, open-label, randomised pilot study to assess two possible routes of faecal microbiota transplant delivery in patients with ulcerative colitis. BMJ Open 2019; 9:e030659. [PMID: 31719078 PMCID: PMC6858155 DOI: 10.1136/bmjopen-2019-030659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Imbalance of the gut microbiome is key to the pathogenesis of ulcerative colitis (UC). Faecal microbiota transplant (FMT) is the transfer of homogenised and filtered faeces from a healthy individual to the gastrointestinal tract of a patient with disease. Published datasets show a positive signal for the use of FMT to treat UC, but the optimal route and dose of FMT remain unanswered. METHODS AND ANALYSIS This prospective, multi-centre open-label, randomised pilot study will assess two possible routes of FMT delivery, via the nasogastric (NG) route or by delivery to the COLON, in 30 patients with active UC recruited from three sites in the UK. Stool will be collected from healthy screened donors, processed, frozen and stored under a Medicines and Healthcare products Regulatory Agency (MHRA) "specials" manufacturing licence held at the University of Birmingham Microbiome Treatment Centre. Thawed FMT samples will be administered to patients either via eight nasogastric infusions given initially over 4 days starting on the day of randomisation, and then again for 4 days in week 4 for foregut delivery (total of 240 g of stool) or via one colonoscopic infusion followed by seven weekly enemas according to the hindgut protocol (total of 360 g of stool). Patients will be followed up weekly for 8 weeks, and then at 12 weeks. The aims of this pilot study are (1) to determine which FMT administration route (NG or COLON) should be investigated in a randomised double-blind, placebo-controlled trial and (2) to determine if a full randomised controlled trial is feasible. The primary outcome will be a composite assessment of both qualitative and quantitative data based on efficacy (clinical response), acceptability and safety. At the end of the pilot study, decisions will be made regarding the feasibility of a full randomised double-blind, placebo-controlled trial and, if deemed feasible, which route of administration should be used in such a study. ETHICS AND DISSEMINATION Ethical approval for this study has been obtained from the East Midlands-Nottingham Research Ethics Committee (REC 17/EM/0274). At the end of the study, findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals. TRIAL REGISTRATION NUMBER ISRCTN74072945.
Collapse
Affiliation(s)
- Mohammed Nabil Nabil Quraishi
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham, UK
| | - Mehmet Yalchin
- Department of Gastroenterology, St Marks Hospital, London, UK
| | | | - Jonathan Segal
- Department of Gastroenterology, St Marks Hospital, London, UK
| | - Naveen Sharma
- Department of Gastroenterology, Heart of England NHS Foundation Trust, Birmingham, UK
| | - Peter Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Victoria McCune
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Public Health Laboratory Birmingham, Public Health England Midlands and East Region, Birmingham, UK
| | - Ailsa L Hart
- Department of Gastroenterology, St Marks Hospital, London, UK
| | - Daniel Gaya
- Gastroenterology Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Natalie J Ives
- Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Laura Magill
- Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Shrushma Loi
- Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Catherine Hewitt
- Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, Dentistry and Nursing, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | - Nicholas James Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Royal Hospital for Children Glasgow, Glasgow, UK
| | - Christel McMullan
- Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | - Christopher Quince
- Warwick Medical School, Microbiology and Infection, University of Warwick, Coventry, UK
| | | | - Tariq Iqbal
- University of Birmingham Microbiome Treatment Centre, University of Birmingham, Birmingham, UK
- Department of Gastroenterology, Queen Elizabeth Hospital, Birmingham, UK
| |
Collapse
|
26
|
Gerasimidis K, Svolos V, Nichols B, Papadopoulou R, Quince C, Ijaz UZ, Milling S, Gaya DR, Russell RK, Hansen R. Reply. Gastroenterology 2019; 157:1161-1162. [PMID: 31408620 DOI: 10.1053/j.gastro.2019.08.015] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/08/2019] [Indexed: 12/02/2022]
Affiliation(s)
- Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Vaios Svolos
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Ben Nichols
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, UK
| | | | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK
| | - Simon Milling
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel R Gaya
- Department of Gastroenterology, Glasgow Royal Infirmary, Glasgow, UK
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, UK
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, UK
| |
Collapse
|
27
|
Yang C, Pei X, Wu Y, Yan L, Yan Y, Song Y, Coyle NM, Martinez-Urtaza J, Quince C, Hu Q, Jiang M, Feil E, Yang D, Song Y, Zhou D, Yang R, Falush D, Cui Y. Recent mixing of Vibrio parahaemolyticus populations. ISME J 2019; 13:2578-2588. [PMID: 31235840 PMCID: PMC6775990 DOI: 10.1038/s41396-019-0461-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 01/24/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 02/07/2023]
Abstract
Humans have profoundly affected the ocean environment but little is known about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found in warm coastal waters and causes gastroenteritis in humans and economically significant disease in shrimps. Based on data from 1103 genomes of environmental and clinical isolates, we show that V. parahaemolyticus is divided into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are largely restricted to the US and Northern Europe, while the others are found worldwide, with VppAsia making up the great majority of isolates in the seas around Asia. Patterns of diversity within and between the populations are consistent with them having arisen by progressive divergence via genetic drift during geographical isolation. However, we find that there is substantial overlap in their current distribution. These observations can be reconciled without requiring genetic barriers to exchange between populations if long-range dispersal has increased dramatically in the recent past. We found that VppAsia isolates from the US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within epidemic lineages, we estimate that recombination affects about 0.017% of the genome per year, implying that the genetic mixture has taken place within the last few decades. These results suggest that human activity, such as shipping, aquatic products trade and increased human migration between continents, are responsible for the change of distribution pattern of this species.
Collapse
Affiliation(s)
- Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xiaoyan Pei
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lin Yan
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yuqin Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | | | | | | | - Qinghua Hu
- Shenzhen Centre for Disease Control and Prevention, Shenzhen, 518055, China
| | - Min Jiang
- Shenzhen Centre for Disease Control and Prevention, Shenzhen, 518055, China
| | | | - Dajin Yang
- National Center for Food Safety Risk Assessment, Beijing, 100022, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | | | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| |
Collapse
|
28
|
Svolos V, Hansen R, Nichols B, Quince C, Ijaz UZ, Papadopoulou RT, Edwards CA, Watson D, Alghamdi A, Brejnrod A, Ansalone C, Duncan H, Gervais L, Tayler R, Salmond J, Bolognini D, Klopfleisch R, Gaya DR, Milling S, Russell RK, Gerasimidis K. Treatment of Active Crohn's Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition. Gastroenterology 2019; 156:1354-1367.e6. [PMID: 30550821 DOI: 10.1053/j.gastro.2018.12.002] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [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: 06/03/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Exclusive enteral nutrition (EEN) is the only established dietary treatment for Crohn's disease (CD), but its acceptability is limited. There is a need for novel dietary treatments for CD. METHODS We evaluated the effects of an individualized food-based diet (CD-TREAT), with similar composition to EEN, on the gut microbiome, inflammation, and clinical response in a rat model, healthy adults, and children with relapsing CD. Twenty-five healthy adults randomly received EEN or CD-TREAT for 7 days, followed by a 14-day washout period, followed by the alternate diet. Fecal microbiome and metabolome were assessed before and after each diet. HLA-B7 and HLA-B27 transgenic rats with gut inflammation received EEN, CD-TREAT, or standard chow for 4 weeks. Fecal, luminal, and tissue microbiome, fecal metabolites, and gut inflammation were assessed. Five children with active CD activity received CD-TREAT and their clinical activity and calprotectin were evaluated after 8 weeks of treatment. RESULTS For healthy adults, CD-TREAT was easier to comply with and more acceptable than EEN. CD-TREAT induced similar effects to EEN (EEN vs CD-TREAT) on fecal microbiome composition, metabolome, mean total sulfide (increase 133.0 ± 80.5 vs 54.3 ± 47.0 nmol/g), pH (increase 1.3 ± 0.5 vs 0.9 ± 0.6), and the short-chain fatty acids (μmol/g) acetate (decrease 27.4 ± 22.6 vs 21.6 ± 20.4), propionate (decrease 5.7 ± 7.8 vs 5.2 ± 7.9), and butyrate (decrease 7.0 ± 7.4 vs 10.2 ± 8.5). In the rat model, CD-TREAT and EEN produced similar changes in bacterial load (decrease 0.3 ± 0.3 log10 16S rRNA gene copies per gram), short-chain fatty acids, microbiome, and ileitis severity (mean histopathology score decreases of 1.25 for EEN [P = .015] and 1.0 for CD-TREAT [P = .044] vs chow). In children receiving CD-TREAT, 4 (80%) had a clinical response and 3 (60%) entered remission, with significant concurrent decreases in fecal calprotectin (mean decrease 918 ± 555 mg/kg; P = .002). CONCLUSION CD-TREAT replicates EEN changes in the microbiome, decreases gut inflammation, is well tolerated, and is potentially effective in patients with active CD. ClinicalTrials.gov, numbers NCT02426567 and NCT03171246.
Collapse
Affiliation(s)
- Vaios Svolos
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom
| | - Ben Nichols
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | | | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Rodanthi T Papadopoulou
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Christine A Edwards
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - David Watson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Adel Alghamdi
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Asker Brejnrod
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Cecilia Ansalone
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Hazel Duncan
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom
| | - Lisa Gervais
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom
| | - Rachel Tayler
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom
| | | | - Daniele Bolognini
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Daniel R Gaya
- Department of Gastroenterology, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Simon Milling
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Royal Hospital for Children, Glasgow, United Kingdom
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, Dentistry & Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow, United Kingdom.
| |
Collapse
|
29
|
Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell 2019; 176:649-662.e20. [PMID: 30661755 PMCID: PMC6349461 DOI: 10.1016/j.cell.2019.01.001] [Citation(s) in RCA: 782] [Impact Index Per Article: 156.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/15/2018] [Accepted: 12/28/2018] [Indexed: 02/06/2023]
Abstract
The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.
Collapse
Affiliation(s)
| | | | - Serena Manara
- CIBIO Department, University of Trento, Trento, Italy
| | - Moreno Zolfo
- CIBIO Department, University of Trento, Trento, Italy
| | | | | | | | - Paolo Manghi
- CIBIO Department, University of Trento, Trento, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, Trento, Italy
| | - Paolo Ghensi
- CIBIO Department, University of Trento, Trento, Italy
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council, Valencia, Spain
| | | | - Casey DuLong
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | | | | | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute, Cambridge, MA, USA
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy.
| |
Collapse
|
30
|
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Author Correction: Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 2018; 3:963. [PMID: 30042441 PMCID: PMC7608358 DOI: 10.1038/s41564-018-0209-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | | | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sonny Tm Lee
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA. .,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
31
|
Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M. Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Curr Biol 2018; 28:2420-2428.e10. [PMID: 30033331 PMCID: PMC6089836 DOI: 10.1016/j.cub.2018.05.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/09/2018] [Accepted: 05/18/2018] [Indexed: 02/04/2023]
Abstract
Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20th-century observations in Eastern Europe [3, 4] suggest that Paratyphi C enteric fever may once have had a wide-ranging impact on human societies. Here, we describe a draft Paratyphi C genome (Ragna) recovered from the 800-year-old skeleton (SK152) of a young woman in Trondheim, Norway. Paratyphi C sequences were recovered from her teeth and bones, suggesting that she died of enteric fever and demonstrating that these bacteria have long caused invasive salmonellosis in Europeans. Comparative analyses against modern Salmonella genome sequences revealed that Paratyphi C is a clade within the Para C lineage, which also includes serovars Choleraesuis, Typhisuis, and Lomita. Although Paratyphi C only infects humans, Choleraesuis causes septicemia in pigs and boar [5] (and occasionally humans), and Typhisuis causes epidemic swine salmonellosis (chronic paratyphoid) in domestic pigs [2, 3]. These different host specificities likely evolved in Europe over the last ∼4,000 years since the time of their most recent common ancestor (tMRCA) and are possibly associated with the differential acquisitions of two genomic islands, SPI-6 and SPI-7. The tMRCAs of these bacterial clades coincide with the timing of pig domestication in Europe [6]. Salmonella enterica aDNA sequences were found within 800-year-old teeth and bone The invasive Para C lineage was defined from 50,000 modern S. enterica genomes The Para C lineage includes Ragna, the aDNA genome, and human and swine pathogens Only few genomic changes occurred in the Para C lineage over its 3,000-year history
Collapse
Affiliation(s)
- Zhemin Zhou
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| | - Inge Lundstrøm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Alicia Tran-Dien
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nabil-Fareed Alikhan
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Martin J Sergeant
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | | | - Anna K Fotakis
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | | | - Stian S Hamre
- Department of Archaeology, History, Cultural Studies and Religion, University of Bergen, Post Box 7805, 5020 Bergen, Norway
| | - Sherwood Casjens
- Pathology Department, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | | | - Christopher Quince
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | | | | | - Simon Y W Ho
- School of Life and Environmental Sciences; University of Sydney, Sydney NSW 2006, Australia
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; NTNU University Museum, N-7491 Trondheim, Norway.
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK.
| |
Collapse
|
32
|
Delmont TO, Quince C, Shaiber A, Esen ÖC, Lee ST, Rappé MS, McLellan SL, Lücker S, Eren AM. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 2018; 3:804-813. [PMID: 29891866 PMCID: PMC6792437 DOI: 10.1038/s41564-018-0176-9] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [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: 05/25/2017] [Accepted: 05/15/2018] [Indexed: 01/28/2023]
Abstract
Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean.
Collapse
Affiliation(s)
- Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | | | - Alon Shaiber
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - Özcan C Esen
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sonny Tm Lee
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Michael S Rappé
- Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sebastian Lücker
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA. .,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
33
|
Joyce A, Ijaz UZ, Nzeteu C, Vaughan A, Shirran SL, Botting CH, Quince C, O'Flaherty V, Abram F. Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass. Front Microbiol 2018; 9:540. [PMID: 29619022 PMCID: PMC5871674 DOI: 10.3389/fmicb.2018.00540] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 10/17/2017] [Accepted: 03/09/2018] [Indexed: 11/13/2022] Open
Abstract
Harvesting valuable bioproducts from various renewable feedstocks is necessary for the critical development of a sustainable bioeconomy. Anaerobic digestion is a well-established technology for the conversion of wastewater and solid feedstocks to energy with the additional potential for production of process intermediates of high market values (e.g., carboxylates). In recent years, first-generation biofuels typically derived from food crops have been widely utilized as a renewable source of energy. The environmental and socioeconomic limitations of such strategy, however, have led to the development of second-generation biofuels utilizing, amongst other feedstocks, lignocellulosic biomass. In this context, the anaerobic digestion of perennial grass holds great promise for the conversion of sustainable renewable feedstock to energy and other process intermediates. The advancement of this technology however, and its implementation for industrial applications, relies on a greater understanding of the microbiome underpinning the process. To this end, microbial communities recovered from replicated anaerobic bioreactors digesting grass were analyzed. The bioreactors leachates were not buffered and acidic pH (between 5.5 and 6.3) prevailed at the time of sampling as a result of microbial activities. Community composition and transcriptionally active taxa were examined using 16S rRNA sequencing and microbial functions were investigated using metaproteomics. Bioreactor fraction, i.e., grass or leachate, was found to be the main discriminator of community analysis across the three molecular level of investigation (DNA, RNA, and proteins). Six taxa, namely Bacteroidia, Betaproteobacteria, Clostridia, Gammaproteobacteria, Methanomicrobia, and Negativicutes accounted for the large majority of the three datasets. The initial stages of grass hydrolysis were carried out by Bacteroidia, Gammaproteobacteria, and Negativicutes in the grass biofilms, in addition to Clostridia in the bioreactor leachates. Numerous glycolytic enzymes and carbohydrate transporters were detected throughout the bioreactors in addition to proteins involved in butanol and lactate production. Finally, evidence of the prevalence of stressful conditions within the bioreactors and particularly impacting Clostridia was observed in the metaproteomes. Taken together, this study highlights the functional importance of Clostridia during the anaerobic digestion of grass and thus research avenues allowing members of this taxon to thrive should be explored.
Collapse
Affiliation(s)
- Aoife Joyce
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Umer Z Ijaz
- Environmental Omics Laboratory, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Corine Nzeteu
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.,Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aoife Vaughan
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Sally L Shirran
- Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St Andrews, Fife, United Kingdom
| | - Christopher Quince
- Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| |
Collapse
|
34
|
Heidrich ES, Dolfing J, Wade MJ, Sloan WT, Quince C, Curtis TP. Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry 2018. [PMID: 28910698 DOI: 10.1016/j.biolectrochem.2017.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The factors that affect microbial community assembly and its effects on the performance of bioelectrochemical systems are poorly understood. Sixteen microbial fuel cell (MFC) reactors were set up to test the importance of inoculum, temperature and substrate: Arctic soil versus wastewater as inoculum; warm (26.5°C) versus cold (7.5°C) temperature; and acetate versus wastewater as substrate. Substrate was the dominant factor in determining performance and diversity: unexpectedly the simple electrogenic substrate delivered a higher diversity than a complex wastewater. Furthermore, in acetate fed reactors, diversity did not correlate with performance, yet in wastewater fed ones it did, with greater diversity sustaining higher power densities and coulombic efficiencies. Temperature had only a minor effect on power density, (Q10: 2 and 1.2 for acetate and wastewater respectively): this is surprising given the well-known temperature sensitivity of anaerobic bioreactors. Reactors were able to operate at low temperature with real wastewater without the need for specialised inocula; it is speculated that MFC biofilms may have a self-heating effect. Importantly, the warm acetate fed reactors in this study did not act as direct model for cold wastewater fed systems. Application of this technology will encompass use of real wastewater at ambient temperatures.
Collapse
Affiliation(s)
- E S Heidrich
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - J Dolfing
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - M J Wade
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - W T Sloan
- Department of Civil Engineering, University of Glasgow, Glasgow G12 8LT, UK
| | - C Quince
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - T P Curtis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| |
Collapse
|
35
|
Heidrich E, Dolfing J, Wade M, Sloan W, Quince C, Curtis T. Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells. Bioelectrochemistry 2018; 119:43-50. [DOI: 10.1016/j.bioelechem.2017.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/21/2017] [Accepted: 07/14/2017] [Indexed: 11/29/2022]
|
36
|
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods 2017; 14:1063-1071. [PMID: 28967888 DOI: 10.1101/099127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/25/2017] [Indexed: 05/25/2023]
Abstract
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
Collapse
Affiliation(s)
- Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Peter Hofmann
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Peter Belmann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, Oregon, USA
| | - Stefan Janssen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Department of Pediatrics, University of California, San Diego, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - Johannes Dröge
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ivan Gregor
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Stephan Majda
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
| | - Jessika Fiedler
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Eik Dahms
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Bremges
- Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ruben Garrido-Oter
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Matthew Z DeMaere
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rayan Chikhi
- Department of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, France
- National Centre of the Scientific Research (CNRS), Rennes, France
| | - Niranjan Nagarajan
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Christopher Quince
- Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fernando Meyer
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Monika Balvočiūtė
- Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Søren J Sørensen
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Burton K H Chia
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Bertrand Denis
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Jeff L Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Zhong Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Robert Egan
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Dongwan Don Kang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Charles Deltel
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Claire Lemaitre
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Pierre Peterlongo
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Guillaume Rizk
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
- Algorizk-IT consulting and software systems, Paris, France
| | - Dominique Lavenier
- National Centre of the Scientific Research (CNRS), Rennes, France
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, California, USA
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chirag Jain
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marc Strous
- Energy Engineering and Geomicrobiology, University of Calgary, Calgary, Alberta, Canada
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael D Barton
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hsin-Hung Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | | | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, New York, New York, USA
| | - Vitor C Piro
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
- Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alice C McHardy
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS)
| |
Collapse
|
37
|
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nat Methods 2017; 14:1063-1071. [PMID: 28967888 DOI: 10.1038/nmeth.4458] [Citation(s) in RCA: 430] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/25/2017] [Indexed: 12/12/2022]
Abstract
Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
Collapse
Affiliation(s)
- Alexander Sczyrba
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Peter Hofmann
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Peter Belmann
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - David Koslicki
- Mathematics Department, Oregon State University, Corvallis, Oregon, USA
| | - Stefan Janssen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Department of Pediatrics, University of California, San Diego, California, USA.,Department of Computer Science and Engineering, University of California, San Diego, California, USA
| | - Johannes Dröge
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ivan Gregor
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Stephan Majda
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany
| | - Jessika Fiedler
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Eik Dahms
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Andreas Bremges
- Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Ruben Garrido-Oter
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Tue Sparholt Jørgensen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark.,Department of Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Yang Bai
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dmitrij Turaev
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Matthew Z DeMaere
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Rayan Chikhi
- Department of Computer Science, Research Center in Computer Science (CRIStAL), Signal and Automatic Control of Lille, Lille, France.,National Centre of the Scientific Research (CNRS), Rennes, France
| | - Niranjan Nagarajan
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Christopher Quince
- Department of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, UK
| | - Fernando Meyer
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Monika Balvočiūtė
- Department of Computer Science, University of Tuebingen, Tuebingen, Germany
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Section of Environmental microbiology and Biotechnology, Aarhus University, Roskilde, Denmark
| | - Søren J Sørensen
- Department of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Burton K H Chia
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Bertrand Denis
- Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Jeff L Froula
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Zhong Wang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Robert Egan
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Dongwan Don Kang
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Charles Deltel
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Claire Lemaitre
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Pierre Peterlongo
- GenScale-Bioinformatics Research Team, Inria Rennes-Bretagne Atlantique Research Centre, Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Guillaume Rizk
- Institute of Research in Informatics and Random Systems (IRISA), Rennes, France.,Algorizk-IT consulting and software systems, Paris, France
| | - Dominique Lavenier
- National Centre of the Scientific Research (CNRS), Rennes, France.,Institute of Research in Informatics and Random Systems (IRISA), Rennes, France
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, California, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chirag Jain
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marc Strous
- Energy Engineering and Geomicrobiology, University of Calgary, Calgary, Alberta, Canada
| | - Heiner Klingenberg
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Peter Meinicke
- Department of Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Michael D Barton
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Hsin-Hung Lin
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yu-Chieh Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | | | - Daniel A Cuevas
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Robert A Edwards
- Computational Science Research Center, San Diego State University, San Diego, California, USA
| | - Surya Saha
- Boyce Thompson Institute for Plant Research, New York, New York, USA
| | - Vitor C Piro
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany.,Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Bernhard Y Renard
- Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany
| | - Mihai Pop
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.,Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | | | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
| | - Edward M Rubin
- Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
| | - Aaron E Darling
- The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alice C McHardy
- Formerly Department of Algorithmic Bioinformatics, Heinrich Heine University (HHU), Duesseldorf, Germany.,Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS)
| |
Collapse
|
38
|
Connelly S, Shin SG, Dillon RJ, Ijaz UZ, Quince C, Sloan WT, Collins G. Bioreactor Scalability: Laboratory-Scale Bioreactor Design Influences Performance, Ecology, and Community Physiology in Expanded Granular Sludge Bed Bioreactors. Front Microbiol 2017; 8:664. [PMID: 28507535 PMCID: PMC5410579 DOI: 10.3389/fmicb.2017.00664] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 06/17/2016] [Accepted: 03/31/2017] [Indexed: 11/24/2022] Open
Abstract
Studies investigating the feasibility of new, or improved, biotechnologies, such as wastewater treatment digesters, inevitably start with laboratory-scale trials. However, it is rarely determined whether laboratory-scale results reflect full-scale performance or microbial ecology. The Expanded Granular Sludge Bed (EGSB) bioreactor, which is a high-rate anaerobic digester configuration, was used as a model to address that knowledge gap in this study. Two laboratory-scale idealizations of the EGSB—a one-dimensional and a three- dimensional scale-down of a full-scale design—were built and operated in triplicate under near-identical conditions to a full-scale EGSB. The laboratory-scale bioreactors were seeded using biomass obtained from the full-scale bioreactor, and, spent water from the distillation of whisky from maize was applied as substrate at both scales. Over 70 days, bioreactor performance, microbial ecology, and microbial community physiology were monitored at various depths in the sludge-beds using 16S rRNA gene sequencing (V4 region), specific methanogenic activity (SMA) assays, and a range of physical and chemical monitoring methods. SMA assays indicated dominance of the hydrogenotrophic pathway at full-scale whilst a more balanced activity profile developed during the laboratory-scale trials. At each scale, Methanobacterium was the dominant methanogenic genus present. Bioreactor performance overall was better at laboratory-scale than full-scale. We observed that bioreactor design at laboratory-scale significantly influenced spatial distribution of microbial community physiology and taxonomy in the bioreactor sludge-bed, with 1-D bioreactor types promoting stratification of each. In the 1-D laboratory bioreactors, increased abundance of Firmicutes was associated with both granule position in the sludge bed and increased activity against acetate and ethanol as substrates. We further observed that stratification in the sludge-bed in 1-D laboratory-scale bioreactors was associated with increased richness in the underlying microbial community at species (OTU) level and improved overall performance.
Collapse
Affiliation(s)
- Stephanie Connelly
- Infrastructure and Environment, School of Engineering, University of GlasgowGlasgow, UK
| | - Seung G Shin
- School of Environmental Science and Engineering, Pohang University of Science and TechnologyPohang, South Korea
| | - Robert J Dillon
- Microbial Communities Laboratory, National University of Ireland GalwayGalway, Ireland
| | - Umer Z Ijaz
- Infrastructure and Environment, School of Engineering, University of GlasgowGlasgow, UK
| | | | - William T Sloan
- Infrastructure and Environment, School of Engineering, University of GlasgowGlasgow, UK
| | - Gavin Collins
- Infrastructure and Environment, School of Engineering, University of GlasgowGlasgow, UK.,Microbial Communities Laboratory, National University of Ireland GalwayGalway, Ireland
| |
Collapse
|
39
|
Sinclair L, Ijaz UZ, Jensen LJ, Coolen MJL, Gubry-Rangin C, Chroňáková A, Oulas A, Pavloudi C, Schnetzer J, Weimann A, Ijaz A, Eiler A, Quince C, Pafilis E. Seqenv: linking sequences to environments through text mining. PeerJ 2016; 4:e2690. [PMID: 28028456 PMCID: PMC5178346 DOI: 10.7717/peerj.2690] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 07/26/2016] [Accepted: 10/14/2016] [Indexed: 11/24/2022] Open
Abstract
Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.
Collapse
Affiliation(s)
- Lucas Sinclair
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
| | - Umer Z Ijaz
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Lars Juhl Jensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marco J L Coolen
- Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Department of Chemistry, Curtin University of Technology, Bentley, WA, Australia
| | - Cecile Gubry-Rangin
- Institute of Biological & Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Anastasis Oulas
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| | - Christina Pavloudi
- Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| | - Julia Schnetzer
- Department of Molecular Ecology, Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Aaron Weimann
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ali Ijaz
- Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury, Sydney, Australia
| | - Alexander Eiler
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
| | | | - Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece
| |
Collapse
|
40
|
Ray JL, Althammer J, Skaar KS, Simonelli P, Larsen A, Stoecker D, Sazhin A, Ijaz UZ, Quince C, Nejstgaard JC, Frischer M, Pohnert G, Troedsson C. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities. Mol Ecol 2016; 25:5585-5602. [PMID: 27662431 DOI: 10.1111/mec.13844] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 03/07/2016] [Revised: 08/25/2016] [Accepted: 09/08/2016] [Indexed: 12/01/2022]
Abstract
In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances.
Collapse
Affiliation(s)
- Jessica L Ray
- Hjort Centre for Marine Ecosystem Dynamics, Uni Research Environment, Uni Research AS, Nygårdsgaten 112, Bergen, N-5008, Norway.
| | - Julia Althammer
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07443, Germany
| | - Katrine S Skaar
- Hjort Centre for Marine Ecosystem Dynamics, Uni Research Environment, Uni Research AS, Nygårdsgaten 112, Bergen, N-5008, Norway
| | - Paolo Simonelli
- Department of Biology, University of Bergen, Thormøhlensgt 53A, Bergen, 5006, Norway
| | - Aud Larsen
- Hjort Centre for Marine Ecosystem Dynamics, Uni Research Environment, Uni Research AS, Nygårdsgaten 112, Bergen, N-5008, Norway
| | - Diane Stoecker
- Horn Point Lab, Center of Environmental Science, University of Maryland, Cambridge, MA, 21613, USA
| | - Andrey Sazhin
- Laboratory of Ecology of Plankton Organisms, Russian Academy of Sciences, P.P. Shirshov Institute of Oceanology, Nakhimovsky Prospect 36, Moscow, Russia
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Christopher Quince
- WMS - Microbiology and Infection, University of Warwick Medical School, Coventry, CV4 7AL, UK
| | - Jens C Nejstgaard
- Department 3, Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, Stechlin, OT Neuglobsow, 16775, Germany
| | - Marc Frischer
- Hjort Centre for Marine Ecosystem Dynamics, Uni Research Environment, Uni Research AS, Nygårdsgaten 112, Bergen, N-5008, Norway.,Skidaway Institute of Oceanography, 10 Science Circle, Savannah, GA, 31411, USA
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, Jena, 07443, Germany
| | - Christofer Troedsson
- Hjort Centre for Marine Ecosystem Dynamics, Uni Research Environment, Uni Research AS, Nygårdsgaten 112, Bergen, N-5008, Norway
| |
Collapse
|
41
|
Abstract
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
Collapse
Affiliation(s)
- Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tomáš Flouri
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ben Nichols
- School of Engineering, University of Glasgow , Glasgow , United Kingdom
| | - Christopher Quince
- School of Engineering, University of Glasgow, Glasgow, United Kingdom; Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; UMR LSTM, CIRAD, Montpellier, France
| |
Collapse
|
42
|
Cho SK, Kim DH, Quince C, Im WT, Oh SE, Shin SG. Low-strength ultrasonication positively affects methanogenic granules toward higher AD performance: Implications from microbial community shift. Ultrason Sonochem 2016; 32:198-203. [PMID: 27150761 DOI: 10.1016/j.ultsonch.2016.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/08/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
To elucidate the enhanced methane yield from organic wastes, the effects of low-strength ultrasonication on the microbial community structures in upflow anaerobic sludge blanket reactors were for the first time analyzed using pyrosequencing. Interestingly, a more even microbial community was observed in the ultrasonicated granules than in the control, which could compensate for the decreased richness and resulted in comparable (archaea) or even higher (bacteria) diversity. The ultrasonicated granules contained higher levels of δ-Proteobacteria, of which many are reportedly potential syntrophs, as well as methanogenic genera Methanosaeta, Methanotorris, and Methanococcus. The increased presence of syntrophic bacteria with their methanogenic partners was discussed with respect to hydrogen flux; their selective proliferation seems to be responsible for the enhanced anaerobic performance. This study is the first research shedding light on the novel function of low-strength ultrasound shifting the microbial structure towards better biogas production performance, and will facilitate application of low-strength ultrasound to other bioprocesses.
Collapse
Affiliation(s)
- Si-Kyung Cho
- Department of Biological and Environmental Science, Dongguk University, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do, Republic of Korea
| | - Dong-Hoon Kim
- Department of Civil Engineering, Inha University, 100 Inha-ro, Nam-gu, Incheon, Republic of Korea
| | | | - Wan-Taek Im
- Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong, Gyeonggi-do, Republic of Korea
| | - Sae-Eun Oh
- Department of Environmental Engineering, Hanbat National University, San 16-1, Duckmyoung-dong, Yuseong-gu, Daejeon, Republic of Korea
| | - Seung Gu Shin
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang, Gyeongbuk, Republic of Korea.
| |
Collapse
|
43
|
Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, Calus S, Loman N, Ijaz UZ. The effect of DNA extraction methodology on gut microbiota research applications. BMC Res Notes 2016; 9:365. [PMID: 27456340 PMCID: PMC4960752 DOI: 10.1186/s13104-016-2171-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [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: 05/12/2016] [Accepted: 07/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effect that traditional and modern DNA extraction methods have on applications to study the role of gut microbiota in health and disease is a topic of current interest. Genomic DNA was extracted from three faecal samples and one probiotic capsule using three popular methods; chaotropic (CHAO) method, phenol/chloroform (PHEC) extraction, proprietary kit (QIAG). The performance of each of these methods on DNA yield and quality, microbiota composition using quantitative PCR, deep sequencing of the 16S rRNA gene, and sequencing analysis pipeline was evaluated. RESULTS The CHAO yielded the highest and the QIAG kit the lowest amount of double-stranded DNA, but the purity of isolated nucleic acids was better for the latter method. The CHAO method yielded a higher concentration of bacterial taxa per mass (g) of faeces. Sequencing coverage was higher in CHAO method but a higher proportion of the initial sequencing reads were retained for assignments to operational taxonomic unit (OTU) in the QIAG kit compared to the other methods. The QIAG kit appeared to have longer trimmed reads and shorter regions of worse quality than the other two methods. A distinct separation of α-diversity indices between different DNA extraction methods was not observed. When compositional dissimilarities between samples were explored, a strong separation was observed according to sample type. The effect of the extraction method was either marginal (Bray-Curtis distance) or none (unweighted Unifrac distance). Taxon membership and abundance in each sample was independent of the DNA extraction method used. CONCLUSIONS We have benchmarked several DNA extraction methods commonly used in gut microbiota research and their differences depended on the downstream applications intended for use. Caution should be paid when the intention is to pool and analyse samples or data from studies which have used different DNA extraction methods.
Collapse
Affiliation(s)
- Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | - Martin Bertz
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | | | - Katja Brunner
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | - Alanna Bruce
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | - Emilie Combet
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, Glasgow Royal Infirmary, University of Glasgow, Glasgow, UK
| | - Szymon Calus
- School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Nick Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow, G12 8LT, UK.
| |
Collapse
|
44
|
Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Soyer OS. Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J 2016; 10:2557-2568. [PMID: 27022995 PMCID: PMC5113837 DOI: 10.1038/ismej.2016.45] [Citation(s) in RCA: 377] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022]
Abstract
The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development with mathematical model building. We discuss specific examples where model–experiment integration has already resulted in important insights into MC function and structure. We also highlight key research questions that still demand better integration of experiments and models. We argue that such integration is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved.
Collapse
Affiliation(s)
- Stefanie Widder
- CUBE, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Rosalind J Allen
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Thomas Pfeiffer
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Thomas P Curtis
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - William T Sloan
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, UK
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sam P Brown
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, MA, USA.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wenying Shou
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Helen Kettle
- Biomathematics and Statistics Scotland, Edinburgh, UK
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Andreas F Haas
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Béatrice Laroche
- Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France
| | | | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Kim Milferstedt
- INRA, UR0050, Laboratoire de Biotechnologie de l'Environnement, Narbonne, France
| | - Jan R van der Meer
- Department of Fundamental Microbiology, Université de Lausanne, Lausanne, Switzerland
| | - Tobias Groβkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Jef Huisman
- Department of Aquatic Microbiology, University of Amsterdam, Amsterdam, The Netherlands
| | - Andrew Free
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Cristian Picioreanu
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Isaac Klapper
- Department of Mathematics, Temple University, Philadelphia, PA, USA
| | - Simon Labarthe
- Département de Mathématiques Informatiques Appliquées, INRA, Jouy-en-Josas, France
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Harris Wang
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
| |
Collapse
|
45
|
Haig SJ, Gauchotte-Lindsay C, Collins G, Quince C. Bioaugmentation Mitigates the Impact of Estrogen on Coliform-Grazing Protozoa in Slow Sand Filters. Environ Sci Technol 2016; 50:3101-10. [PMID: 26895622 PMCID: PMC4841604 DOI: 10.1021/acs.est.5b05027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Exposure to endocrine-disrupting chemicals (EDCs), such as estrogens, is a growing issue for human and animal health as they have been shown to cause reproductive and developmental abnormalities in wildlife and plants and have been linked to male infertility disorders in humans. Intensive farming and weather events, such as storms, flash flooding, and landslides, contribute estrogen to waterways used to supply drinking water. This paper explores the impact of estrogen exposure on the performance of slow sand filters (SSFs) used for water treatment. The feasibility and efficacy of SSF bioaugmentation with estrogen-degrading bacteria was also investigated, to determine whether removal of natural estrogens (estrone, estradiol, and estriol) and overall SSF performance for drinking water treatment could be improved. Strains for SSF augmentation were isolated from full-scale, municipal SSFs so as to optimize survival in the laboratory-scale SSFs used. Concentrations of the natural estrogens, determined by gas chromatography coupled with mass spectrometry (GC-MS), revealed augmented SSFs reduced the overall estrogenic potency of the supplied water by 25% on average and removed significantly more estrone and estradiol than nonaugmented filters. A negative correlation was found between coliform removal and estrogen concentration in nonaugmented filters. This was due to the toxic inhibition of protozoa, indicating that high estrogen concentrations can have functional implications for SSFs (such as impairing coliform removal). Consequently, we suggest that high estrogen concentrations could impact significantly on water quality production and, in particular, on pathogen removal in biological water filters.
Collapse
Affiliation(s)
- Sarah-Jane Haig
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
- Phone: 734-764-6350. E-mail:
| | | | - Gavin Collins
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
- Microbial
Ecophysiology Laboratory, School of Natural Sciences and Ryan Institute, National University of Ireland, Galway, Ireland
| | - Christopher Quince
- School
of Engineering, Rankine Building, University
of Glasgow, Glasgow G12 8LT, U.K.
| |
Collapse
|
46
|
Schirmer M, D'Amore R, Ijaz UZ, Hall N, Quince C. Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data. BMC Bioinformatics 2016; 17:125. [PMID: 26968756 PMCID: PMC4787001 DOI: 10.1186/s12859-016-0976-y] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [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: 10/16/2015] [Accepted: 03/02/2016] [Indexed: 11/17/2022] Open
Abstract
Background Illumina’s sequencing platforms are currently the most utilised sequencing systems worldwide. The technology has rapidly evolved over recent years and provides high throughput at low costs with increasing read-lengths and true paired-end reads. However, data from any sequencing technology contains noise and our understanding of the peculiarities and sequencing errors encountered in Illumina data has lagged behind this rapid development. Results We conducted a systematic investigation of errors and biases in Illumina data based on the largest collection of in vitro metagenomic data sets to date. We evaluated the Genome Analyzer II, HiSeq and MiSeq and tested state-of-the-art low input library preparation methods. Analysing in vitro metagenomic sequencing data allowed us to determine biases directly associated with the actual sequencing process. The position- and nucleotide-specific analysis revealed a substantial bias related to motifs (3mers preceding errors) ending in “GG”. On average the top three motifs were linked to 16 % of all substitution errors. Furthermore, a preferential incorporation of ddGTPs was recorded. We hypothesise that all of these biases are related to the engineered polymerase and ddNTPs which are intrinsic to any sequencing-by-synthesis method. We show that quality-score-based error removal strategies can on average remove 69 % of the substitution errors - however, the motif-bias remains. Conclusion Single-nucleotide polymorphism changes in bacterial genomes can cause significant changes in phenotype, including antibiotic resistance and virulence, detecting them within metagenomes is therefore vital. Current error removal techniques are not designed to target the peculiarities encountered in Illumina sequencing data and other sequencing-by-synthesis methods, causing biases to persist and potentially affect any conclusions drawn from the data. In order to develop effective diagnostic and therapeutic approaches we need to be able to identify systematic sequencing errors and distinguish these errors from true genetic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0976-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. .,Harvard T.H. Chan School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA. .,University of Glasgow, School of Engineering, Oakfield Avenue, Glasgow, G12 8LT, UK.
| | - Rosalinda D'Amore
- University of Liverpool, Centre for Genomic Research, Crown Street, Liverpool, L69 7ZB, UK
| | - Umer Z Ijaz
- University of Glasgow, School of Engineering, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Neil Hall
- University of Liverpool, Centre for Genomic Research, Crown Street, Liverpool, L69 7ZB, UK
| | | |
Collapse
|
47
|
Torondel B, Ensink JHJ, Gundogdu O, Ijaz UZ, Parkhill J, Abdelahi F, Nguyen VA, Sudgen S, Gibson W, Walker AW, Quince C. Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines. Microb Biotechnol 2016; 9:209-23. [PMID: 26875588 PMCID: PMC4767293 DOI: 10.1111/1751-7915.12334] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 03/16/2015] [Revised: 10/02/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Improving the rate and extent of faecal decomposition in basic forms of sanitation such as pit latrines would benefit around 1.7 billion users worldwide, but to do so requires a major advance in our understanding of the biology of these systems. As a critical first step, bacterial diversity and composition was studied in 30 latrines in Tanzania and Vietnam using pyrosequencing of 16S rRNA genes, and correlated with a number of intrinsic environmental factors such as pH, temperature, organic matter content/composition and geographical factors. Clear differences were observed at the operational taxonomic unit, family and phylum level in terms of richness and community composition between latrines in Tanzania and Vietnam. The results also clearly show that environmental variables, particularly substrate type and availability, can exert a strong structuring influence on bacterial communities in latrines from both countries. The origins and significance of these environmental differences are discussed. This work describes the bacterial ecology of pit latrines in combination with inherent latrine characteristics at an unprecedented level of detail. As such, it provides useful baseline information for future studies that aim to understand the factors that affect decomposition rates in pit latrines.
Collapse
Affiliation(s)
- Belen Torondel
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jeroen H J Ensink
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Ozan Gundogdu
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | | | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Faraji Abdelahi
- Ifakara Health Institute, off Mlabani Passage, P.O. Box 53, Ifakara, Tanzania
| | - Viet-Anh Nguyen
- Hanoi University of Civil Engineering, 55 Giai Phong Road, Hanoi, Vietnam
| | - Steven Sudgen
- Environmental Health Group, Department of Disease Control, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Walter Gibson
- Bear Valley Ventures, Braeside, Utkinton Lane, Cotebrook, Tarporley, Cheshire CW6 0JH, UK
| | - Alan W Walker
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK.,Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB21 9SB, UK
| | | |
Collapse
|
48
|
Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ 2016; 4:e1603. [PMID: 26870609 PMCID: PMC4748697 DOI: 10.7717/peerj.1603] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 10/14/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022] Open
Abstract
Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability.PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.
Collapse
Affiliation(s)
- Ivan Gregor
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Johannes Dröge
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Melanie Schirmer
- The Broad Institute of MIT and Harvard , Cambridge, MA , United States
| | | | - Alice C McHardy
- Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Computational Biology of Infection Research, Helmholtz Center for Infection Research, Braunschweig, Germany
| |
Collapse
|
49
|
D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics 2016; 17:55. [PMID: 26763898 PMCID: PMC4712552 DOI: 10.1186/s12864-015-2194-9] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [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: 06/08/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. Results We assembled 2 synthetic communities with an even (EM) and uneven (UM) distribution of archaeal and bacterial strains and species, as metagenomic control material, to assess performance of different experimental strategies. The 2 synthetic communities were used in this study, to highlight the limitations and the advantages of the leading sequencing platforms: MiSeq (Illumina), The Pacific Biosciences RSII, 454 GS-FLX/+ (Roche), and IonTorrent (Life Technologies). We describe an extensive survey based on synthetic communities using 3 experimental designs (fusion primers, universal tailed tag, ligated adaptors) across the 9 hypervariable 16S rDNA regions. We demonstrate that library preparation methodology can affect data interpretation due to different error and chimera rates generated during the procedure. The observed community composition was always biased, to a degree that depended on the platform, sequenced region and primer choice. However, crucially, our analysis suggests that 16S rRNA sequencing is still quantitative, in that relative changes in abundance of taxa between samples can be recovered, despite these biases. Conclusion We have assessed a range of experimental conditions across several next generation sequencing platforms using the most up-to-date configurations. We propose that the choice of sequencing platform and experimental design needs to be taken into consideration in the early stage of a project by running a small trial consisting of several hypervariable regions to quantify the discriminatory power of each region. We also suggest that the use of a synthetic community as a positive control would be beneficial to identify the potential biases and procedural drawbacks that may lead to data misinterpretation. The results of this study will serve as a guideline for making decisions on which experimental condition and sequencing platform to consider to achieve the best microbial profiling. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2194-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rosalinda D'Amore
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | | | - Melanie Schirmer
- School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK.
| | - John G Kenny
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Richard Gregory
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Migun Shakya
- Department of Biological Sciences, Dartmouth College, Hanover, NH03755, USA.
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA.
| | | | - Neil Hall
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
| |
Collapse
|
50
|
Abstract
BACKGROUND VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. RESULTS VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. DISCUSSION VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
Collapse
Affiliation(s)
- Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tomáš Flouri
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ben Nichols
- School of Engineering, University of Glasgow , Glasgow , United Kingdom
| | - Christopher Quince
- School of Engineering, University of Glasgow, Glasgow, United Kingdom; Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; UMR LSTM, CIRAD, Montpellier, France
| |
Collapse
|