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da Silva TF, Glória RDA, de Sousa TJ, Americo MF, Freitas ADS, Viana MVC, de Jesus LCL, da Silva Prado LC, Daniel N, Ménard O, Cochet MF, Dupont D, Jardin J, Borges AD, Fernandes SOA, Cardoso VN, Brenig B, Ferreira E, Profeta R, Aburjaile FF, de Carvalho RDO, Langella P, Le Loir Y, Cherbuy C, Jan G, Azevedo V, Guédon É. Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain. BMC Microbiol 2023; 23:364. [PMID: 38008714 PMCID: PMC10680302 DOI: 10.1186/s12866-023-03112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the well-known probiotic reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis. RESULTS CEC15 mitigates inflammation, reinforces intestinal barrier, and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). Most predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and their intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis. CONCLUSIONS These findings suggest that the CEC15 strain holds promise as a probiotic, as it could modulate the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly some forms of diarrhea.
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Affiliation(s)
- Tales Fernando da Silva
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rafael de Assis Glória
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Jesus de Sousa
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Monique Ferrary Americo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Andria Dos Santos Freitas
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Marcus Vinicius Canário Viana
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Luís Cláudio Lima de Jesus
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Nathalie Daniel
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Olivia Ménard
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Marie-Françoise Cochet
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Didier Dupont
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Julien Jardin
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Amanda Dias Borges
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Simone Odília Antunes Fernandes
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Valbert Nascimento Cardoso
- Department of clinical and toxicological analysis, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Department of Molecular Biology of Livestock, Institute of Veterinary Medicine, Georg-August Universität Göttingen, Göttingen, Germany
| | - Enio Ferreira
- Department of general pathology, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Flavia Figueira Aburjaile
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Veterinary school, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Yves Le Loir
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Claire Cherbuy
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Gwénaël Jan
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France
| | - Vasco Azevedo
- Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Éric Guédon
- 1INRAE, Institut Agro, STLO, UMR1253, 65 rue de Saint Brieuc, 35042, Rennes, Cedex, France.
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Hu D, Fuller NR, Caterson ID, Holmes AJ, Reeves PR. Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Rep 2022; 38:110239. [PMID: 35021078 DOI: 10.1016/j.celrep.2021.110239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 10/17/2021] [Accepted: 12/17/2021] [Indexed: 02/01/2023] Open
Abstract
Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens.
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Affiliation(s)
- Dalong Hu
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia
| | - Nicholas R Fuller
- The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ian D Caterson
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; The Boden Institute, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia; Metabolism and Obesity Services, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Andrew J Holmes
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia
| | - Peter R Reeves
- School of Life and Environmental Sciences, Charles Perkins Centre, University of Sydney, Camperdown, NSW 2006, Australia.
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Delannoy S, Beutin L, Mariani-Kurkdjian P, Fleiss A, Bonacorsi S, Fach P. The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters. Front Cell Infect Microbiol 2017; 7:30. [PMID: 28224115 PMCID: PMC5293828 DOI: 10.3389/fcimb.2017.00030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/23/2017] [Indexed: 01/10/2023] Open
Abstract
Escherichia coli strains belonging to serogroups O1 and O2 are frequently associated with human infections, especially extra-intestinal infections such as bloodstream infections or urinary tract infections. These strains can be associated with a large array of flagellar antigens. Because of their frequency and clinical importance, a reliable detection of E. coli O1 and O2 strains and also the frequently associated K1 capsule is important for diagnosis and source attribution of E. coli infections in humans and animals. By sequencing the O-antigen clusters of various O1 and O2 strains we showed that the serogroups O1 and O2 are encoded by different sets of O-antigen encoding genes and identified potentially new O-groups. We developed qPCR-assays to detect the various O1 and O2 variants and the K1-encoding gene. These qPCR assays proved to be 100% sensitive and 100% specific and could be valuable tools for the investigations of zoonotic and food-borne infection of humans with O1 and O2 extra-intestinal (ExPEC) or Shiga toxin-producing E. coli (STEC) strains.
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Affiliation(s)
- Sabine Delannoy
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR)Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität BerlinBerlin, Germany
| | - Patricia Mariani-Kurkdjian
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Aubin Fleiss
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Stéphane Bonacorsi
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Patrick Fach
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
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Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front Microbiol 2016; 7:644. [PMID: 27199968 PMCID: PMC4853403 DOI: 10.3389/fmicb.2016.00644] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
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Affiliation(s)
- Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University ParkPA, USA
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Gian Marco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, College ParkMD, USA
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