1
|
Zanditenas E, Ankri S. Unraveling the interplay between unicellular parasites and bacterial biofilms: Implications for disease persistence and antibiotic resistance. Virulence 2024; 15:2289775. [PMID: 38058008 PMCID: PMC10761080 DOI: 10.1080/21505594.2023.2289775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023] Open
Abstract
Bacterial biofilms have attracted significant attention due to their involvement in persistent infections, food and water contamination, and infrastructure corrosion. This review delves into the intricate interactions between bacterial biofilms and unicellular parasites, shedding light on their impact on biofilm formation, structure, and function. Unicellular parasites, including protozoa, influence bacterial biofilms through grazing activities, leading to adaptive changes in bacterial communities. Moreover, parasites like Leishmania and Giardia can shape biofilm composition in a grazing independent manner, potentially influencing disease outcomes. Biofilms, acting as reservoirs, enable the survival of protozoan parasites against environmental stressors and antimicrobial agents. Furthermore, these biofilms may influence parasite virulence and stress responses, posing challenges in disease treatment. Interactions between unicellular parasites and fungal-containing biofilms is also discussed, hinting at complex microbial relationships in various ecosystems. Understanding these interactions offers insights into disease mechanisms and antibiotic resistance dissemination, paving the way for innovative therapeutic strategies and ecosystem-level implications.
Collapse
Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| |
Collapse
|
2
|
Cherrak Y, Salazar MA, Näpflin N, Malfertheiner L, Herzog MKM, Schubert C, von Mering C, Hardt WD. Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut. Nat Microbiol 2024:10.1038/s41564-024-01775-x. [PMID: 39160293 DOI: 10.1038/s41564-024-01775-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 07/04/2024] [Indexed: 08/21/2024]
Abstract
Resource competition is a driver of gut microbiota composition. Bacteria can outcompete metabolically similar rivals through the limitation of shared growth-fuelling nutrients. The mechanisms underlying this remain unclear for bacteria with identical sets of metabolic genes. Here we analysed the lactose utilization operon in the murine commensal Escherichia coli 8178. Using in vitro and in vivo approaches, we showed that translation of the lactose utilization repressor gene lacI from its native non-canonical GTG start codon increases the basal expression of the lactose utilization cluster, enhancing adaptation to lactose consumption. Consequently, a strain carrying the wild type lacI GTG start codon outperformed the lacI ATG start codon mutant in the mouse intestine. This advantage was attenuated upon limiting host lactose intake through diet shift or altering the mutant frequency, emphasizing the context-dependent effect of a single nucleotide change on the bacterial fitness of a common member of the gut microbiota. Coupled with a genomic analysis highlighting the selection of non-ATG start codons in sugar utilization regulator genes across the Enterobacteriaceae family, our data exposed an unsuspected function of non-canonical start codons in metabolic competition.
Collapse
Affiliation(s)
- Yassine Cherrak
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Miguel Angel Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Nicolas Näpflin
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Mathias K-M Herzog
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christopher Schubert
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
3
|
Singh S, Gola C, Singh B, Agrawal V, Chaba R. D-galactonate metabolism in enteric bacteria: a molecular and physiological perspective. Curr Opin Microbiol 2024; 81:102524. [PMID: 39137493 DOI: 10.1016/j.mib.2024.102524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024]
Abstract
D-galactonate, a widely prevalent sugar acid, was first reported as a nutrient source for enteric bacteria in the 1970s. Since then, decades of research enabled a description of the modified Entner-Doudoroff pathway involved in its degradation and reported the structural and biochemical features of its metabolic enzymes, primarily in Escherichia coli K-12. However, only in the last few years, the D-galactonate transporter has been characterized, and the regulation of the dgo operon, encoding the structural genes for the transporter and enzymes of D-galactonate metabolism, has been detailed. Notably, in recent years, multiple evolutionary studies have identified the dgo operon as a dominant target for adaptation of E. coli in the mammalian gut. Despite considerable research on dgo operon, numerous fundamental questions remain to be addressed. The emerging relevance of the dgo operon in host-bacterial interactions further necessitates the study of D-galactonate metabolism in other enterobacterial strains.
Collapse
Affiliation(s)
- Swati Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Chetna Gola
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Bhupinder Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India
| | - Vishal Agrawal
- Amity School of Biological Sciences, Amity University Punjab, Mohali, SAS Nagar, Punjab 140306, India
| | - Rachna Chaba
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar, Punjab 140306, India.
| |
Collapse
|
4
|
Hermanson JB, Tolba SA, Chrisler EA, Leone VA. Gut microbes, diet, and genetics as drivers of metabolic liver disease: a narrative review outlining implications for precision medicine. J Nutr Biochem 2024; 133:109704. [PMID: 39029595 DOI: 10.1016/j.jnutbio.2024.109704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/01/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is rapidly increasing in prevalence, impacting over a third of the global population. The advanced form of MASLD, Metabolic dysfunction-associated steatohepatitis (MASH), is on track to become the number one indication for liver transplant. FDA-approved pharmacological agents are limited for MASH, despite over 400 ongoing clinical trials, with only a single drug (resmetirom) currently on the market. This is likely due to the heterogeneous nature of disease pathophysiology, which involves interactions between highly individualized genetic and environmental factors. To apply precision medicine approaches that overcome interpersonal variability, in-depth insights into interactions between genetics, nutrition, and the gut microbiome are needed, given that each have emerged as dynamic contributors to MASLD and MASH pathogenesis. Here, we discuss the associations and molecular underpinnings of several of these factors individually and outline their interactions in the context of both patient-based studies and preclinical animal model systems. Finally, we highlight gaps in knowledge that will require further investigation to aid in successfully implementing precision medicine to prevent and alleviate MASLD and MASH.
Collapse
Affiliation(s)
- Jake B Hermanson
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Samar A Tolba
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Nutrition and Clinical Nutrition, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Evan A Chrisler
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vanessa A Leone
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| |
Collapse
|
5
|
Osbelt L, Almási ÉDH, Wende M, Kienesberger S, Voltz A, Lesker TR, Muthukumarasamy U, Knischewski N, Nordmann E, Bielecka AA, Giralt-Zúñiga M, Kaganovitch E, Kühne C, Baier C, Pietsch M, Müsken M, Greweling-Pils MC, Breinbauer R, Flieger A, Schlüter D, Müller R, Erhardt M, Zechner EL, Strowig T. Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms. Nat Microbiol 2024; 9:1792-1811. [PMID: 38862602 PMCID: PMC11222139 DOI: 10.1038/s41564-024-01710-0] [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: 06/06/2023] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
The Klebsiella oxytoca species complex is part of the human microbiome, especially during infancy and childhood. K. oxytoca species complex strains can produce enterotoxins, namely, tilimycin and tilivalline, while also contributing to colonization resistance (CR). The relationship between these seemingly contradictory roles is not well understood. Here, by coupling ex vivo assays with CRISPR-mutagenesis and various mouse models, we show that K. oxytoca provides CR against Salmonella Typhimurium. In vitro, the antimicrobial activity against various Salmonella strains depended on tilimycin production and was induced by various simple carbohydrates. In vivo, CR against Salmonella depended on toxin production in germ-free mice, while it was largely toxin-independent in mice with residual microbiota. This was linked to the relative levels of toxin-inducing carbohydrates in vivo. Finally, dulcitol utilization was essential for toxin-independent CR in gnotobiotic mice. Together, this demonstrates that nutrient availability is key to both toxin-dependent and substrate-driven competition between K. oxytoca and Salmonella.
Collapse
Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Éva D H Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-von-Guericke University, Magdeburg, Germany
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Voltz
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Nele Knischewski
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elke Nordmann
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - María Giralt-Zúñiga
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Eugen Kaganovitch
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Caroline Kühne
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claas Baier
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Michael Pietsch
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Rolf Breinbauer
- BioTechMed-Graz, Institute of Organic Chemistry, Graz University of Technology, Graz, Austria
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Dirk Schlüter
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Rolf Müller
- Department Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Marc Erhardt
- Institute for Biology-Molecular Microbiology, Humboldt-Universität zu Berlin, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Graz, Austria
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
- German Center for Infection Research (DZIF),Partner Site Hannover-Braunschweig, Braunschweig, Germany.
- Center for Individualized Infection Medicine, Hannover, Germany.
| |
Collapse
|
6
|
Cottam C, White RT, Beck LC, Stewart CJ, Beatson SA, Lowe EC, Grinter R, Connolly JPR. Metabolism of L-arabinose converges with virulence regulation to promote enteric pathogen fitness. Nat Commun 2024; 15:4462. [PMID: 38796512 PMCID: PMC11127945 DOI: 10.1038/s41467-024-48933-7] [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: 12/18/2023] [Accepted: 05/16/2024] [Indexed: 05/28/2024] Open
Abstract
Virulence and metabolism are often interlinked to control the expression of essential colonisation factors in response to host-associated signals. Here, we identified an uncharacterised transporter of the dietary monosaccharide ʟ-arabinose that is widely encoded by the zoonotic pathogen enterohaemorrhagic Escherichia coli (EHEC), required for full competitive fitness in the mouse gut and highly expressed during human infection. Discovery of this transporter suggested that EHEC strains have an enhanced ability to scavenge ʟ-arabinose and therefore prompted us to investigate the impact of this nutrient on pathogenesis. Accordingly, we discovered that ʟ-arabinose enhances expression of the EHEC type 3 secretion system, increasing its ability to colonise host cells, and that the underlying mechanism is dependent on products of its catabolism rather than the sensing of ʟ-arabinose as a signal. Furthermore, using the murine pathogen Citrobacter rodentium, we show that ʟ-arabinose metabolism provides a fitness benefit during infection via virulence factor regulation, as opposed to supporting pathogen growth. Finally, we show that this mechanism is not restricted to ʟ-arabinose and extends to other pentose sugars with a similar metabolic fate. This work highlights the importance integrating central metabolism with virulence regulation in order to maximise competitive fitness of enteric pathogens within the host-niche.
Collapse
Affiliation(s)
- Curtis Cottam
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys T White
- Institute of Environmental Science and Research, Wellington, New Zealand
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Lauren C Beck
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Christopher J Stewart
- Newcastle University Translation and Clinical Research Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Elisabeth C Lowe
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, NE2 4HH, Newcastle-upon-Tyne, UK.
| |
Collapse
|
7
|
Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe 2024; 32:739-754.e4. [PMID: 38565143 PMCID: PMC11081829 DOI: 10.1016/j.chom.2024.03.005] [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: 10/16/2023] [Revised: 02/06/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.
Collapse
Affiliation(s)
- Joshua M Kirsch
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA
| | - Andrew J Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA; Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045, USA.
| |
Collapse
|
8
|
Dankittipong N, Broek JVD, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Transmission rates of veterinary and clinically important antibiotic resistant Escherichia coli: A meta- ANALYSIS. Prev Vet Med 2024; 225:106156. [PMID: 38402649 DOI: 10.1016/j.prevetmed.2024.106156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
The transmission rate per hour between hosts is a key parameter for simulating transmission dynamics of antibiotic-resistant bacteria, and might differ for antibiotic resistance genes, animal species, and antibiotic usage. We conducted a Bayesian meta-analysis of resistant Escherichia coli (E. coli) transmission in broilers and piglets to obtain insight in factors determining the transmission rate, infectious period, and reproduction ratio. We included blaCTX-M-1, blaCTX-M-2, blaOXA-162, catA1, mcr-1, and fluoroquinolone resistant E. coli. The Maximum a Posteriori (MAP) transmission rate in broilers without antibiotic treatment ranged from 0.4∙10-3 to 2.5∙10-3 depending on type of broiler (SPF vs conventional) and inoculation strains. For piglets, the MAP in groups without antibiotic treatment were between 0.7∙10-3 and 0.8∙10-3, increasing to 0.9∙10-3 in the group with antibiotic treatment. In groups without antibiotic treatment, the transmission rate of resistant E. coli in broilers was almost twice the transmission rate in piglets. Amoxicillin increased the transmission rate of E. coli carrying blaCTX-M-2 by three-fold. The MAP infectious period of resistant E. coli in piglets with and without antibiotics is between 971 and 1065 hours (40 - 43 days). The MAP infectious period of resistant E. coli in broiler without antibiotics is between 475 and 2306 hours (20 - 96 days). The MAP infectious period of resistant E. coli in broiler with antibiotics is between 2702 and 3462 hours (113 - 144 days) which means a lifelong colonization. The MAP basic reproduction ratio in piglets of infection with resistant E. coli when using antibiotics is 27.70, which is higher than MAP in piglets without antibiotics between 15.65 and 18.19. The MAP basic reproduction ratio in broilers ranges between 3.46 and 92.38. We consider three possible explanations for our finding that in the absence of antibiotics the transmission rate is higher among broilers than among piglets: i) due to the gut microbiome of animals, ii) fitness costs of bacteria, and iii) differences in experimental set-up between the studies. Regarding infectious period and reproduction ratio, the effect of the resistance gene, antibiotic treatment, and animal species are inconclusive due to limited data.
Collapse
Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
| |
Collapse
|
9
|
Doranga S, Conway T. Nitrogen assimilation by E. coli in the mammalian intestine. mBio 2024; 15:e0002524. [PMID: 38380942 PMCID: PMC10936423 DOI: 10.1128/mbio.00025-24] [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: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Nitrogen is an essential element for all living organisms, including Escherichia coli. Potential nitrogen sources are abundant in the intestine, but knowledge of those used specifically by E. coli to colonize remains limited. Here, we sought to determine the specific nitrogen sources used by E. coli to colonize the streptomycin-treated mouse intestine. We began by investigating whether nitrogen is limiting in the intestine. The NtrBC two-component system upregulates approximately 100 genes in response to nitrogen limitation. We showed that NtrBC is crucial for E. coli colonization, although most genes of the NtrBC regulon are not induced, which indicates that nitrogen is not limiting in the intestine. RNA-seq identified upregulated genes in colonized E. coli involved in transport and catabolism of seven amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine. Competitive colonization experiments revealed that L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides serve as nitrogen sources for E. coli in the intestine. Furthermore, the colonization defect of a L-serine deaminase mutant was rescued by excess nitrogen in the drinking water but not by an excess of carbon and energy, demonstrating that L-serine serves primarily as a nitrogen source. Similar rescue experiments showed that N-acetylneuraminic acid serves as both a carbon and nitrogen source. To a minor extent, aspartate and ammonia also serve as nitrogen sources. Overall, these findings demonstrate that E. coli utilizes multiple nitrogen sources for successful colonization of the mouse intestine, the most important of which is L-serine. IMPORTANCE While much is known about the carbon and energy sources that are used by E. coli to colonize the mammalian intestine, very little is known about the sources of nitrogen. Interrogation of colonized E. coli by RNA-seq revealed that nitrogen is not limiting, indicating an abundance of nitrogen sources in the intestine. Pathways for assimilation of nitrogen from several amino acids, dipeptides and tripeptides, purines, pyrimidines, urea, and ethanolamine were induced in mice. Competitive colonization assays confirmed that mutants lacking catabolic pathways for L-serine, N-acetylneuraminic acid, N-acetylglucosamine, and di- and tripeptides had colonization defects. Rescue experiments in mice showed that L-serine serves primarily as a nitrogen source, whereas N-acetylneuraminic acid provides both carbon and nitrogen. Of the many nitrogen assimilation mutants tested, the largest colonization defect was for an L-serine deaminase mutant, which demonstrates L-serine is the most important nitrogen source for colonized E. coli.
Collapse
Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
10
|
Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561241. [PMID: 37873088 PMCID: PMC10592638 DOI: 10.1101/2023.10.06.561241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to insertion "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.
Collapse
Affiliation(s)
- Joshua M. Kirsch
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53706, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado - Anschutz Medical Campus, School of Medicine, Aurora, Colorado, 80045, USA
| |
Collapse
|
11
|
Belà B, Di Simone D, Pignataro G, Fusaro I, Gramenzi A. Effects of L. reuteri NBF 2 DSM 32264 Consumption on the Body Weight, Body Condition Score, Fecal Parameters, and Intestinal Microbiota of Healthy Persian Cats. Vet Sci 2024; 11:61. [PMID: 38393079 PMCID: PMC10893002 DOI: 10.3390/vetsci11020061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/13/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
In the literature, there are several studies showing the effects of different probiotic administrations in dogs, while there is limited information about their effects in cats. Furthermore, there are no studies that examined the effects of the probiotic strain Lactobacillus reuteri on cats' welfare, especially considering a specific breed. In this study, the effects of L. reuteri NBF 2 DSM 32264 on body weight, body condition score (BCS), and fecal parameters (fecal score and fecal moisture) of healthy Persian cats were assessed; additionally, a microbiological analysis was carried out to quantify bacterial species like Escherichia coli (for the total coliform count) and Lactobacilli. The administration of L. reuteri NBF 2 DSM 32264 showed no alteration in the body weight and body condition score of Persian cats. The fecal moisture decreased at the end of the study and the values of fecal score were improved. Moreover, at the end of the study period, an increase in Lactobacilli (p > 0.001) was observed. The data collected report the ability of L. reuteri NBF 2 DSM 32264 to improve fecal quality parameters in healthy adult Persian cats, leading to an increase in Lactobacilli and a reduction in total coliforms.
Collapse
Affiliation(s)
- Benedetta Belà
- Department of Veterinary Medicine, University of Teramo, Piano d’Accio, 64100 Teramo, Italy; (G.P.); (I.F.); (A.G.)
| | - Daniele Di Simone
- Department of Economics and Finance, University of Bari, Largo Abbazia Santa Scolastica 53, 70124 Bari, Italy;
| | - Giulia Pignataro
- Department of Veterinary Medicine, University of Teramo, Piano d’Accio, 64100 Teramo, Italy; (G.P.); (I.F.); (A.G.)
| | - Isa Fusaro
- Department of Veterinary Medicine, University of Teramo, Piano d’Accio, 64100 Teramo, Italy; (G.P.); (I.F.); (A.G.)
| | - Alessandro Gramenzi
- Department of Veterinary Medicine, University of Teramo, Piano d’Accio, 64100 Teramo, Italy; (G.P.); (I.F.); (A.G.)
| |
Collapse
|
12
|
Oliveira A, Dias C, Oliveira R, Almeida C, Fuciños P, Sillankorva S, Oliveira H. Paving the way forward: Escherichia coli bacteriophages in a One Health approach. Crit Rev Microbiol 2024; 50:87-104. [PMID: 36608263 DOI: 10.1080/1040841x.2022.2161869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023]
Abstract
Escherichia coli is one of the most notorious pathogens for its ability to adapt, colonize, and proliferate in different habitats through a multitude of acquired virulence factors. Its presence affects the food-processing industry and causes food poisoning, being also a major economic burden for the food, agriculture, and health sectors. Bacteriophages are emerging as an appealing strategy to mitigate bacterial pathogens, including specific E. coli pathovars, without exerting a deleterious effect on humans and animals. This review globally analyzes the applied research on E. coli phages for veterinary, food, and human use. It starts by describing the pathogenic E. coli pathotypes and their relevance in human and animal context. The idea that phages can be used as a One Health approach to control and interrupt the transmission routes of pathogenic E. coli is sustained through an exhaustive revision of the recent literature. The emerging phage formulations, genetic engineering and encapsulation technologies are also discussed as a means of improving phage-based control strategies, with a particular focus on E. coli pathogens.
Collapse
Affiliation(s)
- Ana Oliveira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Carla Dias
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Ricardo Oliveira
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vairão, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Carina Almeida
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Vairão, Vila do Conde, Portugal
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Pablo Fuciños
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | - Sanna Sillankorva
- INL - International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga, Braga, Portugal
| | - Hugo Oliveira
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| |
Collapse
|
13
|
Doranga S, Krogfelt KA, Cohen PS, Conway T. Nutrition of Escherichia coli within the intestinal microbiome. EcoSal Plus 2024:eesp00062023. [PMID: 38417452 DOI: 10.1128/ecosalplus.esp-0006-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/03/2023] [Indexed: 03/01/2024]
Abstract
In this chapter, we update our 2004 review of "The Life of Commensal Escherichia coli in the Mammalian Intestine" (https://doi.org/10.1128/ecosalplus.8.3.1.2), with a change of title that reflects the current focus on "Nutrition of E. coli within the Intestinal Microbiome." The earlier part of the previous two decades saw incremental improvements in understanding the carbon and energy sources that E. coli and Salmonella use to support intestinal colonization. Along with these investigations of electron donors came a better understanding of the electron acceptors that support the respiration of these facultative anaerobes in the gastrointestinal tract. Hundreds of recent papers add to what was known about the nutrition of commensal and pathogenic enteric bacteria. The fact that each biotype or pathotype grows on a different subset of the available nutrients suggested a mechanism for succession of commensal colonizers and invasion by enteric pathogens. Competition for nutrients in the intestine has also come to be recognized as one basis for colonization resistance, in which colonized strain(s) prevent colonization by a challenger. In the past decade, detailed investigations of fiber- and mucin-degrading anaerobes added greatly to our understanding of how complex polysaccharides support the hundreds of intestinal microbiome species. It is now clear that facultative anaerobes, which usually cannot degrade complex polysaccharides, live in symbiosis with the anaerobic degraders. This concept led to the "restaurant hypothesis," which emphasizes that facultative bacteria, such as E. coli, colonize the intestine as members of mixed biofilms and obtain the sugars they need for growth locally through cross-feeding from polysaccharide-degrading anaerobes. Each restaurant represents an intestinal niche. Competition for those niches determines whether or not invaders are able to overcome colonization resistance and become established. Topics centered on the nutritional basis of intestinal colonization and gastrointestinal health are explored here in detail.
Collapse
Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Karen A Krogfelt
- Department of Science and Environment, Pandemix Center Roskilde University, Roskilde, Denmark
| | - Paul S Cohen
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
14
|
Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
Collapse
Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | |
Collapse
|
15
|
Ambat A, Antony L, Maji A, Ghimire S, Mattiello S, Kashyap PC, More S, Sebastian V, Scaria J. Enhancing recovery from gut microbiome dysbiosis and alleviating DSS-induced colitis in mice with a consortium of rare short-chain fatty acid-producing bacteria. Gut Microbes 2024; 16:2382324. [PMID: 39069899 PMCID: PMC11290756 DOI: 10.1080/19490976.2024.2382324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/24/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
The human gut microbiota is a complex community comprising hundreds of species, with a few present in high abundance and the vast majority in low abundance. The biological functions and effects of these low-abundant species on their hosts are not yet fully understood. In this study, we assembled a bacterial consortium (SC-4) consisting of B. paravirosa, C. comes, M. indica, and A. butyriciproducens, which are low-abundant, short-chain fatty acid (SCFA)-producing bacteria isolated from healthy human gut, and tested its effect on host health using germ-free and human microbiota-associated colitis mouse models. The selection also favored these four bacteria being reduced in abundance in either Ulcerative Colitis (UC) or Crohn's disease (CD) metagenome samples. Our findings demonstrate that SC-4 can colonize germ-free (GF) mice, increasing mucin thickness by activating MUC-1 and MUC-2 genes, thereby protecting GF mice from Dextran Sodium Sulfate (DSS)-induced colitis. Moreover, SC-4 aided in the recovery of human microbiota-associated mice from DSS-induced colitis, and intriguingly, its administration enhanced the alpha diversity of the gut microbiome, shifting the community composition closer to control levels. The results showed enhanced phenotypes across all measures when the mice were supplemented with inulin as a dietary fiber source alongside SC-4 administration. We also showed a functional redundancy existing in the gut microbiome, resulting in the low abundant SCFA producers acting as a form of insurance, which in turn accelerates recovery from the dysbiotic state upon the administration of SC-4. SC-4 colonization also upregulated iNOS gene expression, further supporting its ability to produce an increasing number of goblet cells. Collectively, our results provide evidence that low-abundant SCFA-producing species in the gut may offer a novel therapeutic approach to IBD.
Collapse
Affiliation(s)
- Achuthan Ambat
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| | - Linto Antony
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Abhijit Maji
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Sudeep Ghimire
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Samara Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
| | - Purna C. Kashyap
- Enteric Neuroscience Program, Department of Medicine and Physiology, Mayo Clinic, Rochester, MN, USA
| | - Sunil More
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| | - Vanessa Sebastian
- Department of Pathology, Jubilee Mission Medical College and Research Institute, Thrissur, India
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| |
Collapse
|
16
|
Zan L, Zhang W, Shang S, Cui Y, Pei J, Yuan Y, Yue T. Alleviating effect of selenium-enriched Lactobacillus plantarum 6076 on dextran sulfate sodium-induced colitis and liver inflammation in mice. Food Funct 2023; 14:10151-10162. [PMID: 37902068 DOI: 10.1039/d3fo03842d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
The aim of this study is to investigate the alleviating effect of selenium-enriched Lactobacillus plantarum (SL) 6076 on colitis and liver inflammation induced by sodium dextran sulfate (DSS) in mice and its potential molecular mechanisms. Lactobacillus plantarum (LA) was cultured for 3 generations on MRS medium containing sodium selenite to generate SL. LA (3.2 × 1011 CFU mL-1), low selenium Lactobacillus plantarum (LS) (3.9 × 1010 CFU mL-1, 0.35 mg mL-1 Se) and high selenium Lactobacillus plantarum (HS) (2.8 × 1010 CFU mL-1, 0.52 mg mL-1 Se) were continuously fed to mice for 21 d to observe their effects on DSS-induced colitis and liver inflammation in mice. The composition of gut microbiota was detected through high-throughput 16S rRNA sequencing, and inflammatory cytokines, oxidative stress parameters, and serum biochemical indicators were measured in the colon and liver using quantitative polymerase chain reaction (qPCR) and biochemical analysis methods. The results showed that SL alleviated inflammation symptoms in the colon and liver, reduced the expression of inflammatory factors in the colon and liver, regulated oxidative stress responses in the colon, downregulated NF-κB-P65 pathway factors, and altered the composition and structure of the gut microbiota. In summary, DSS-induced colitis may cause liver inflammation, and SL had a significant relieving effect on both colon and liver inflammation. The intervention effect of SL was better than that of LA, while HS was better than LS. SL had a significant alleviating effect on DSS-induced colitis, and may exert its therapeutic effect by downregulating NF-κB-P65 signaling pathways and regulating the structure of intestinal microbiota. This study provides a new approach for the treatment of colitis.
Collapse
Affiliation(s)
- Lixia Zan
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
- College of Biological Sciences and Engineering, Shaanxi Province Key Laboratory of Bio-resources, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723000, China
| | - Wenyi Zhang
- College of Biological Sciences and Engineering, Shaanxi Province Key Laboratory of Bio-resources, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723000, China
| | - Shufeng Shang
- College of Biological Sciences and Engineering, Shaanxi Province Key Laboratory of Bio-resources, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723000, China
| | - Yuanyuan Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
| | - Jinjin Pei
- College of Biological Sciences and Engineering, Shaanxi Province Key Laboratory of Bio-resources, QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723000, China
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| |
Collapse
|
17
|
Gomez-Ramirez U, Nolasco-Romero CG, Contreras-Rodríguez A, Zuñiga G, Mendoza-Elizalde S, Prado-Galbarro FJ, Pérez Aguilar F, Pedraza Tinoco JE, Valencia-Mayoral P, Velázquez-Guadarrama N. Dysbiosis by Eradication of Helicobacter pylori Infection Associated with Follicular Gastropathy and Pangastropathy. Microorganisms 2023; 11:2748. [PMID: 38004759 PMCID: PMC10673246 DOI: 10.3390/microorganisms11112748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Dysbiosis plays an important role in the development of bacterial infections in the gastric mucosa, particularly Helicobacter pylori. The international guidelines for the treatment of H. pylori infections suggest standard triple therapy (STT). Nevertheless, because of the increasing resistance rates to clarithromycin, metronidazole has been widely considered in several countries. Unfortunately, the non-justified administration of antibiotics induces dysbiosis in the target organ. We characterized the gastric microbiota of patients diagnosed with follicular gastropathy and pangastropathy attributed to H. pylori infection, before and after the administration of STT with metronidazole. Dominant relative abundances of Cutibacterium were observed in pre-treatment patients, whereas H. pylori was observed at <11%, suggesting the multifactor property of the disease. The correlation of Cutibacterium acnes and H. pylori with gastric infectious diseases was also evaluated using quantitative real-time polymerase chain reaction. The dominance of C. acnes over H. pylori was observed in gastritis, gastropathies, and non-significant histological alterations. None of the microorganisms were detected in the intestinal metaplasia. Post-treatment alterations revealed an increase in the relative abundances of Staphylococcus, Pseudomonas, and Klebsiella. Non-H. pylori gastrointestinal bacteria can be associated with the initiation and development of gastric diseases, such as pathobiont C. acnes.
Collapse
Affiliation(s)
- Uriel Gomez-Ramirez
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (C.G.N.-R.); (S.M.-E.)
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Carolina G. Nolasco-Romero
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (C.G.N.-R.); (S.M.-E.)
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Gerardo Zuñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Sandra Mendoza-Elizalde
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (C.G.N.-R.); (S.M.-E.)
| | | | - Fernando Pérez Aguilar
- Servicio de Endoscopía Gastrointestinal, Hospital General Dr. Fernando Quiroz, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Mexico City 01140, Mexico;
| | | | - Pedro Valencia-Mayoral
- Departamento de Patología Clínica y Experimental, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico
| | - Norma Velázquez-Guadarrama
- Laboratorio de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Mexico City 06720, Mexico; (U.G.-R.); (C.G.N.-R.); (S.M.-E.)
| |
Collapse
|
18
|
Dey P, Ray Chaudhuri S. The opportunistic nature of gut commensal microbiota. Crit Rev Microbiol 2023; 49:739-763. [PMID: 36256871 DOI: 10.1080/1040841x.2022.2133987] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/30/2022] [Accepted: 10/05/2022] [Indexed: 11/03/2022]
Abstract
The abundance of gut commensals has historically been associated with health-promoting effects despite the fact that the definition of good or bad microbiota remains condition-specific. The beneficial or pathogenic nature of microbiota is generally dictated by the dimensions of host-microbiota and microbe-microbe interactions. With the increasing popularity of gut microbiota in human health and disease, emerging evidence suggests opportunistic infections promoted by those gut bacteria that are generally considered beneficial. Therefore, the current review deals with the opportunistic nature of the gut commensals and aims to summarise the concepts behind the occasional commensal-to-pathogenic transformation of the gut microbes. Specifically, relevant clinical and experimental studies have been discussed on the overgrowth and bacteraemia caused by commensals. Three key processes and their underlying mechanisms have been summarised to be responsible for the opportunistic nature of commensals, viz. improved colonisation fitness that is dictated by commensal-pathogen interactions and availability of preferred nutrients; pathoadaptive mutations that can trigger the commensal-to-pathogen transformation; and evasion of host immune response as a survival and proliferation strategy of the microbes. Collectively, this review provides an updated concept summary on the underlying mechanisms of disease causative events driven by gut commensal bacteria.
Collapse
Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Saumya Ray Chaudhuri
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh, India
| |
Collapse
|
19
|
Cutajar J, Gkrania-Klotsas E, Sander C, Floto A, Chandra A, Manson A, Kumararatne D. Respiratory infectious burden in a cohort of antibody deficiency patients treated with immunoglobulin replacement therapy: The impact of lung pathology and gastroesophageal reflux disease. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100133. [PMID: 37781665 PMCID: PMC10509975 DOI: 10.1016/j.jacig.2023.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 10/03/2023]
Abstract
Background Antibody deficiencies result from reduced immunoglobulin levels and function, increasing susceptibility to, primarily, bacterial infection. Primary antibody deficiencies comprise intrinsic defects in B-cell physiology, often due to inherited errors. Hematological malignancies or B-cell suppressive therapy are major causes of secondary antibody deficiency. Although immunoglobulin replacement therapy (IGRT) reduces infectious burden in antibody deficiency patients, respiratory tract infections remain a significant health burden. We hypothesize that lung pathology and gastroesophageal reflux disease (GORD) increase the risk of pneumonia in antibody deficiency patients, as in the general population. Objective For our cohort of patients with primary antibody deficiency and secondary antibody deficiency, we reviewed their respiratory infectious burden and the impact of lung pathologies and GORD. Methods The medical records of 231 patients on IGRT at a tertiary referral center, from October 26, 2014, to February 19, 2021, were reviewed to determine microbial isolates from sputum samples and prevalence of common lung pathologies and GORD. Results Haemophilus and Pseudomonas species represent a large infectious burden, being identified in 30.2% and 21.4% of sputum samples demonstrating growth, respectively; filamentous fungal and mycobacterial infections were rare. Diagnosed lung pathology increased the proportion of patients with Pseudomonas, Klebsiella, Stenotrophomonas, and Candida species isolated in their sputum, and diagnosed GORD increased the proportion with Enterobacter and Candida species isolated. Conclusions Bacterial respiratory infectious burden remains in primary antibody deficiency and secondary antibody deficiency despite IGRT. Lung pathologies encourage growth of species less susceptible to IGRT, so specialist respiratory medicine input and additional treatments such as inhaled antibiotics are indicated to optimize respiratory outcomes.
Collapse
Affiliation(s)
- Jonathan Cutajar
- John Radcliffe Hospital, Department of Medicine, Oxford, United Kingdom
| | | | - Clare Sander
- Addenbrooke’s Hospital, Respiratory Medicine, Cambridge, United Kingdom
| | - Andres Floto
- Royal Papworth Hospital, Cambridge Centre for Lung Infection, Cambridge, United Kingdom
| | - Anita Chandra
- Addenbrooke’s Hospital, Clinical Immunology, Cambridge, United Kingdom
| | - Ania Manson
- Addenbrooke’s Hospital, Clinical Immunology, Cambridge, United Kingdom
| | | |
Collapse
|
20
|
Zanditenas E, Trebicz-Geffen M, Kolli D, Domínguez-García L, Farhi E, Linde L, Romero D, Chapman M, Kolodkin-Gal I, Ankri S. Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity. NPJ Biofilms Microbiomes 2023; 9:77. [PMID: 37813896 PMCID: PMC10562373 DOI: 10.1038/s41522-023-00444-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
Collapse
Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Divya Kolli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Einan Farhi
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Liat Linde
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Matthew Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
| |
Collapse
|
21
|
Dankittipong N, Alderliesten JB, Van den Broek J, Dame-Korevaar MA, Brouwer MSM, Velkers FC, Bossers A, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Prev Vet Med 2023; 219:105998. [PMID: 37647719 DOI: 10.1016/j.prevetmed.2023.105998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria comparable to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed over 12 pens on the day of hatch (day 0). On day 5, half of the 10 remaining chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). To evaluate the effect of antibiotic treatment, amoxicillin was given twice daily in drinking water in 6 of the 12 pens from days 2-6. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or by other differences between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2-6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
Collapse
Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jesse B Alderliesten
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - M Anita Dame-Korevaar
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Alex Bossers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
| |
Collapse
|
22
|
Gupta U, Dey P. Rise of the guardians: Gut microbial maneuvers in bacterial infections. Life Sci 2023; 330:121993. [PMID: 37536616 DOI: 10.1016/j.lfs.2023.121993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
AIMS Bacterial infections are one of the major causes of mortality globally. The gut microbiota, primarily comprised of the commensals, performs an important role in maintaining intestinal immunometabolic homeostasis. The current review aims to provide a comprehensive understanding of how modulation of the gut microbiota influences opportunistic bacterial infections. MATERIALS AND METHODS Primarily centered around mechanisms related to colonization resistance, nutrient, and metabolite-associated factors, mucosal immune response, and commensal-pathogen reciprocal interactions, we discuss how gut microbiota can promote or prevent bacterial infections. KEY FINDINGS Opportunistic infections can occur directly due to obligate pathogens or indirectly due to the overgrowth of opportunistic pathobionts. Gut microbiota-centered mechanisms of altered intestinal immunometabolic and metabolomic homeostasis play a significant role in infection promotion and prevention. Depletion in the population of commensals, increased abundance of pathobionts, and overall decrease in gut microbial diversity and richness caused due to prolonged antibiotic use are risk factors of opportunistic bacterial infections, including infections from multidrug-resistant spp. Gut commensals can limit opportunistic infections by mechanisms including the production of antimicrobials, short-chain fatty acids, bile acid metabolism, promoting mucin formation, and maintaining immunological balance at the mucosa. Gut microbiota-centered strategies, including the administration of probiotics and fecal microbiota transplantation, could help attenuate opportunistic bacterial infections. SIGNIFICANCE The current review discussed the gut microbial population and function-specific aspects contributing to bacterial infection susceptibility and prophylaxis. Collectively, this review provides a comprehensive understanding of the mechanisms related to the dual role of gut microbiota in bacterial infections.
Collapse
Affiliation(s)
- Upasana Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
| |
Collapse
|
23
|
Zhang M, Luo X, Li X, Zhang T, Wu F, Li M, Lu R, Zhang Y. L-arabinose affects the growth, biofilm formation, motility, c-di-GMP metabolism, and global gene expression of Vibrio parahaemolyticus. J Bacteriol 2023; 205:e0010023. [PMID: 37655915 PMCID: PMC10521368 DOI: 10.1128/jb.00100-23] [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: 03/15/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023] Open
Abstract
The L-arabinose inducible pBAD vectors are commonly used to turn on and off the expression of specific genes in bacteria. The utilization of certain carbohydrates can influence bacterial growth, virulence factor production, and biofilm formation. Vibrio parahaemolyticus, the causative agent of seafood-associated gastroenteritis, can grow in media with L-arabinose as the sole carbon source. However, the effects of L-arabinose on V. parahaemolyticus physiology have not been investigated. In this study, we show that the growth rate, biofilm formation capacity, capsular polysaccharide production, motility, and c-di-GMP production of V. parahaemolyticus are negatively affected by L-arabinose. RNA-seq data revealed significant changes in the expression levels of 752 genes, accounting for approximately 15.6% of V. parahaemolyticus genes in the presence of L-arabinose. The affected genes included those associated with L-arabinose utilization, major virulence genes, known key biofilm-related genes, and numerous regulatory genes. In the majority of type III secretion system, two genes were upregulated in the presence of L-arabinose, whereas in those of type VI secretion system, two genes were downregulated. Ten putative c-di-GMP metabolism-associated genes were also significantly differentially expressed, which may account for the reduced c-di-GMP levels in the presence of L-arabinose. Most importantly, almost 40 putative regulators were significantly differentially expressed due to the induction by L-arabinose, indicating that the utilization of L-arabinose is strictly regulated by regulatory networks in V. parahaemolyticus. The findings increase the understanding of how L-arabinose affects the physiology of V. parahaemolyticus. Researchers should use caution when considering the use of L-arabinose inducible pBAD vectors in V. parahaemolyticus. IMPORTANCE The data in this study show that L-arabinose negatively affects the growth rate, biofilm formation, capsular polysaccharide production, motility, and c-di-GMP production of V. parahaemolyticus. The data also clarify the gene expression profiles of the bacterium in the presence of L-arabinose. Significantly differentially expressed genes in response to L-arabinose were involved in multiple cellular pathways, including L-arabinose utilization, virulence factor production, biofilm formation, motility, adaptation, and regulation. The collective findings indicate the significant impact of L-arabinose on the physiology of V. parahaemolyticus. There may be similar effects on other species of bacteria. Necessary controls should be established when pBAD vectors must be used for ectopic gene expression.
Collapse
Affiliation(s)
- Miaomiao Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Xi Luo
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Xue Li
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Tingting Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
- School of Medicine, Nantong University, Nantong, Jiangsu, China
| | - Fei Wu
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Min Li
- Department of Gastroenterology and Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Renfei Lu
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| | - Yiquan Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, Jiangsu, China
| |
Collapse
|
24
|
Guevara-Ramírez P, Cadena-Ullauri S, Paz-Cruz E, Tamayo-Trujillo R, Ruiz-Pozo VA, Zambrano AK. Role of the gut microbiota in hematologic cancer. Front Microbiol 2023; 14:1185787. [PMID: 37692399 PMCID: PMC10485363 DOI: 10.3389/fmicb.2023.1185787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023] Open
Abstract
Hematologic neoplasms represent 6.5% of all cancers worldwide. They are characterized by the uncontrolled growth of hematopoietic and lymphoid cells and a decreased immune system efficacy. Pathological conditions in hematologic cancer could disrupt the balance of the gut microbiota, potentially promoting the proliferation of opportunistic pathogens. In this review, we highlight studies that analyzed and described the role of gut microbiota in different types of hematologic diseases. For instance, myeloma is often associated with Pseudomonas aeruginosa and Clostridium leptum, while in leukemias, Streptococcus is the most common genus, and Lachnospiraceae and Ruminococcaceae are less prevalent. Lymphoma exhibits a moderate reduction in microbiota diversity. Moreover, certain factors such as delivery mode, diet, and other environmental factors can alter the diversity of the microbiota, leading to dysbiosis. This dysbiosis may inhibit the immune response and increase susceptibility to cancer. A comprehensive analysis of microbiota-cancer interactions may be useful for disease management and provide valuable information on host-microbiota dynamics, as well as the possible use of microbiota as a distinguishable marker for cancer progression.
Collapse
|
25
|
Doranga S, Conway T. OmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine. Microbiol Spectr 2023; 11:e0524122. [PMID: 37014216 PMCID: PMC10269588 DOI: 10.1128/spectrum.05241-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for envZ missense mutants that outcompeted the wild type. The better-colonizing envZ mutants had a higher level of OmpC and reduced OmpF. This suggested the EnvZ/OmpR two-component system and outer membrane proteins play a role in colonization. In this study, we show that wild-type E. coli MG1655 outcompetes an envZ-ompR knockout mutant. Moreover, ompA and ompC knockout mutants are outcompeted by the wild type, while an ompF knockout mutant colonizes better than the wild type. Outer membrane protein gels show the ompF mutant overproduces OmpC. An ompC mutant is more sensitive to bile salts than the wild type and ompF mutant. The ompC mutant initiates colonization slowly because it is sensitive to physiological concentrations of bile salts in the intestine. Overexpression of ompC under the control of a constitutive promoter confers a colonization advantage only when ompF is deleted. These results indicate that fine-tuning of OmpC and OmpF levels is needed to maximize competitive fitness in the intestine. RNA sequencing reveals the EnvZ/OmpR two-component system is active in the intestine: ompC is upregulated and ompF is downregulated. While other factors could also contribute to the advantage provided by OmpC, we provide evidence that OmpC is important for E. coli to colonize the intestine because its smaller pore size excludes bile salts or other unknown toxic substances, while OmpF is deleterious because its larger pore size allows bile salts or other unknown toxic substances to enter the periplasm. IMPORTANCE Every mammalian intestine is colonized with Escherichia coli. Although E. coli is one of the most studied model organisms, how it colonizes the intestine is not fully understood. Here, we investigated the role of the EnvZ/OmpR two-component system and outer membrane proteins in colonization of the mouse intestine by E. coli. We report that an ompC mutant is a poor colonizer, while an ompF mutant, which overproduces OmpC, outcompetes the wild type. OmpF has a larger pore size that allows toxic bile salts or other toxic compounds into the cell and is deleterious for colonization of the intestine. OmpC has a smaller pore size and excludes bile salts. Our findings provide insights into why E. coli fine-tunes the levels of OmpC and OmpF during colonization via the EnvZ/OmpR two-component system.
Collapse
Affiliation(s)
- Sudhir Doranga
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| |
Collapse
|
26
|
Yu L, Gao Y, Ye Z, Duan H, Zhao J, Zhang H, Narbad A, Tian F, Zhai Q, Chen W. Interaction of beta-glucans with gut microbiota: Dietary origins, structures, degradation, metabolism, and beneficial function. Crit Rev Food Sci Nutr 2023:1-26. [PMID: 37272431 DOI: 10.1080/10408398.2023.2217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Beta-glucan (BG), a polysaccharide comprised of interfacing glucose monomers joined via beta-glycosidic linkages, can be defined as a type of dietary fiber with high specificity based on its interaction with the gut microbiota. It can induce similar interindividual microbiota responses, thereby having beneficial effects on the human body. In this paper, we review the four main sources of BG (cereals, fungi, algae, and bacteria) and their differences in structure and content. The interaction of BG with gut microbiota and the resulting health effects have been highlighted, including immune enhancement, regulation of serum cholesterol and insulin levels, alleviation of obesity and improvement of cognitive disorders. Finally, the application of BG in food products and its beneficial effects on the gut microbiota of consumers were discussed. Although some of the mechanisms of action remain unclear, revealing the beneficial functions of BG from the perspective of gut microbiota can help provide theoretical support for the development of diets that target the regulation of microbiota.
Collapse
Affiliation(s)
- Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
| | - Yuhang Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zi Ye
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Arjan Narbad
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
- Gut Health and Microbiome Institute Strategic Programme, Quadram Institute Bioscience, Norwich, UK
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| |
Collapse
|
27
|
Saif NA, Hashem YA, Amin HM, Aziz RK. In Silico and In Vitro Investigation of the Distribution and Expression of Key Genes in the Fucose Operon of Escherichia coli. Microorganisms 2023; 11:1265. [PMID: 37317239 DOI: 10.3390/microorganisms11051265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/22/2023] [Indexed: 06/16/2023] Open
Abstract
Many gut bacteria degrade polysaccharides, providing nutritional advantages to their hosts. Fucose, a mucin degradation product, was suggested as a communication molecule between the resident microbiota and external pathogens. However, the precise role and variants of the fucose utilization pathway remain to be elucidated. Here, we computationally and experimentally investigated the fucose utilization operon of E. coli. While the operon is conserved among E. coli genomes, a variant pathway, in which an ABC transporter system replaces the fucose permease gene (fucP), was computationally identified in 50 out of 1058 genomes. Comparative genomics and subsystems analysis results were confirmed by polymerase chain reaction-based screening of 40 human E. coli isolates, which indicated the conservation of fucP in 92.5% of the isolates (vs. 7.5% of its suggested alternative, yjfF). The in silico predictions were confirmed by in vitro experiments comparing the growth of E. coli strains K12, BL21, and isogenic fucose-utilization K12 mutants. Additionally, fucP and fucI transcripts were quantified in E. coli K12 and BL21, after in silico analysis of their expression in 483 public transcriptomes. In conclusion, E. coli utilizes fucose by two pathway variants, with measurable transcriptional differences. Future studies will explore this variation's impact on signaling and virulence.
Collapse
Affiliation(s)
- Nehal A Saif
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Yomna A Hashem
- Department of Microbiology, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, Cairo 11837, Egypt
| | - Heba M Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza 12451, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Center for Genome and Microbiome Research, Cairo University, Cairo 11562, Egypt
- Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, Cairo 11617, Egypt
| |
Collapse
|
28
|
Carroll-Portillo A, Rumsey KN, Braun CA, Lin DM, Coffman CN, Alcock JA, Singh SB, Lin HC. Mucin and Agitation Shape Predation of Escherichia coli by Lytic Coliphage. Microorganisms 2023; 11:microorganisms11020508. [PMID: 36838472 PMCID: PMC9966288 DOI: 10.3390/microorganisms11020508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
The ability of bacteriophage (phage), abundant within the gastrointestinal microbiome, to regulate bacterial populations within the same micro-environment offers prophylactic and therapeutic opportunities. Bacteria and phage have both been shown to interact intimately with mucin, and these interactions invariably effect the outcomes of phage predation within the intestine. To better understand the influence of the gastrointestinal micro-environment on phage predation, we employed enclosed, in vitro systems to investigate the roles of mucin concentration and agitation as a function of phage type and number on bacterial killing. Using two lytic coliphage, T4 and PhiX174, bacterial viability was quantified following exposure to phages at different multiplicities of infection (MOI) within increasing, physiological levels of mucin (0-4%) with and without agitation. Comparison of bacterial viability outcomes demonstrated that at low MOI, agitation in combination with higher mucin concentration (>2%) inhibited phage predation by both phages. However, when MOI was increased, PhiX predation was recovered regardless of mucin concentration or agitation. In contrast, only constant agitation of samples containing a high MOI of T4 demonstrated phage predation; briefly agitated samples remained hindered. Our results demonstrate that each phage-bacteria pairing is uniquely influenced by environmental factors, and these should be considered when determining the potential efficacy of phage predation under homeostatic or therapeutic circumstances.
Collapse
Affiliation(s)
- Amanda Carroll-Portillo
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
| | - Kellin N. Rumsey
- Statistical Sciences, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Cody A. Braun
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, USA
| | - Derek M. Lin
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, USA
| | | | - Joe A. Alcock
- Department of Emergency Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Sudha B. Singh
- Biomedical Research Institute of New Mexico, Albuquerque, NM 87108, USA
| | - Henry C. Lin
- Division of Gastroenterology and Hepatology, University of New Mexico, Albuquerque, NM 87131, USA
- Medicine Service, New Mexico VA Health Care System, Albuquerque, NM 87108, USA
| |
Collapse
|
29
|
Laganenka L, Lee JW, Malfertheiner L, Dieterich CL, Fuchs L, Piel J, von Mering C, Sourjik V, Hardt WD. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 2023; 8:204-217. [PMID: 36624229 DOI: 10.1038/s41564-022-01286-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Bacteria communicate and coordinate their behaviour at the intra- and interspecies levels by producing and sensing diverse extracellular small molecules called autoinducers. Autoinducer 2 (AI-2) is produced and detected by a variety of bacteria and thus plays an important role in interspecies communication and chemotaxis. Although AI-2 is a major autoinducer molecule present in the mammalian gut and can influence the composition of the murine gut microbiota, its role in bacteria-bacteria and bacteria-host interactions during gut colonization remains unclear. Combining competitive infections in C57BL/6 mice with microscopy and bioinformatic approaches, we show that chemotaxis (cheY) and AI-2 signalling (via lsrB) promote gut colonization by Escherichia coli, which is in turn connected to the ability of the bacteria to utilize fructoselysine (frl operon). We further show that the genomic diversity of E. coli strains with respect to AI-2 signalling allows ecological niche segregation and stable co-existence of different E. coli strains in the mammalian gut.
Collapse
Affiliation(s)
- Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jae-Woo Lee
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Lea Fuchs
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
| | | |
Collapse
|
30
|
Moreira de Gouveia MI, Daniel J, Garrivier A, Bernalier-Donadille A, Jubelin G. Diversity of ethanolamine utilization by human commensal Escherichiacoli. Res Microbiol 2023; 174:103989. [PMID: 35988812 DOI: 10.1016/j.resmic.2022.103989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Ethanolamine (EA) is a substrate naturally present in the human gut and its catabolism by bacteria relies on the presence of eut genes encoding specific metabolic enzymes and accessory proteins. To date, EA utilization has been mostly investigated in gut bacterial pathogens. The aim of this study was to evaluate the ability of human gut commensal Escherichia coli isolates to utilize EA as a nitrogen and/or carbon sources. Although the capacity to consume EA is heterogeneous between the 40 strains of our collection, we determined that most of them could degrade EA to generate ammonia, a useful nitrogen resource for growth. Three isolates were also able to exploit EA as a carbon source. We also revealed that the inability of some strains to catabolize EA is explained either by mutations in the eut locus or by a defect in gene transcription. Finally, we demonstrated the importance of EA utilization for an optimal fitness of commensal E. coli in vivo. Our study provides new insights on the diversity of commensal E. coli strains to utilize EA as a nutrient in the gut and opens the way for new research in the field of interactions between host, gut microbiota and pathogens.
Collapse
Affiliation(s)
| | - Julien Daniel
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | - Annie Garrivier
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| | | | - Gregory Jubelin
- Université Clermont Auvergne, INRAE, MEDIS UMR454, F-63000, Clermont-Ferrand, France.
| |
Collapse
|
31
|
van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
Collapse
Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| |
Collapse
|
32
|
Alvarenga BO, Paiva JB, Souza AI, Rodrigues DR, Tizioto PC, Ferreira AJP. Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces. Poult Sci 2022; 102:102401. [PMID: 36565637 PMCID: PMC9800314 DOI: 10.1016/j.psj.2022.102401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.
Collapse
Affiliation(s)
| | | | | | - Denise R. Rodrigues
- Department of Inspection of Animal Products, Ministry of Agriculture, Livestock and Food Supply (MAPA), Brasília, Brazil
| | | | - Antonio J. Piantino Ferreira
- School of Veterinary Medicine and Animal Science of University of São Paulo, São Paulo, Brazil,Corresponding author:
| |
Collapse
|
33
|
Geurtsen J, de Been M, Weerdenburg E, Zomer A, McNally A, Poolman J. Genomics and pathotypes of the many faces of Escherichia coli. FEMS Microbiol Rev 2022; 46:6617594. [PMID: 35749579 PMCID: PMC9629502 DOI: 10.1093/femsre/fuac031] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 06/22/2022] [Indexed: 01/09/2023] Open
Abstract
Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.
Collapse
Affiliation(s)
- Jeroen Geurtsen
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | - Mark de Been
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| | | | - Aldert Zomer
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 Utrecht, the Netherlands
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, B15 2TT Birmingham, United Kingdom
| | - Jan Poolman
- Janssen Vaccines and Prevention B.V., 2333 Leiden, the Netherlands
| |
Collapse
|
34
|
Sauvaitre T, Van Landuyt J, Durif C, Roussel C, Sivignon A, Chalancon S, Uriot O, Van Herreweghen F, Van de Wiele T, Etienne-Mesmin L, Blanquet-Diot S. Role of mucus-bacteria interactions in Enterotoxigenic Escherichia coli (ETEC) H10407 virulence and interplay with human microbiome. NPJ Biofilms Microbiomes 2022; 8:86. [PMID: 36266277 PMCID: PMC9584927 DOI: 10.1038/s41522-022-00344-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
The intestinal mucus layer has a dual role in human health constituting a well-known microbial niche that supports gut microbiota maintenance but also acting as a physical barrier against enteric pathogens. Enterotoxigenic Escherichia coli (ETEC), the major agent responsible for traveler's diarrhea, is able to bind and degrade intestinal mucins, representing an important but understudied virulent trait of the pathogen. Using a set of complementary in vitro approaches simulating the human digestive environment, this study aimed to describe how the mucus microenvironment could shape different aspects of the human ETEC strain H10407 pathophysiology, namely its survival, adhesion, virulence gene expression, interleukin-8 induction and interactions with human fecal microbiota. Using the TNO gastrointestinal model (TIM-1) simulating the physicochemical conditions of the human upper gastrointestinal (GI) tract, we reported that mucus secretion and physical surface sustained ETEC survival, probably by helping it to face GI stresses. When integrating the host part in Caco2/HT29-MTX co-culture model, we demonstrated that mucus secreting-cells favored ETEC adhesion and virulence gene expression, but did not impede ETEC Interleukin-8 (IL-8) induction. Furthermore, we proved that mucosal surface did not favor ETEC colonization in a complex gut microbial background simulated in batch fecal experiments. However, the mucus-specific microbiota was widely modified upon the ETEC challenge suggesting its role in the pathogen infectious cycle. Using multi-targeted in vitro approaches, this study supports the major role played by mucus in ETEC pathophysiology, opening avenues in the design of new treatment strategies.
Collapse
Affiliation(s)
- Thomas Sauvaitre
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France.,Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Josefien Van Landuyt
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Claude Durif
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Charlène Roussel
- Université Laval, Nutrition and Functional Foods Institute (INAF), 2440 Bd Hochelaga Suite 1710, Québec, QC, G1V 0A6, Canada
| | - Adeline Sivignon
- Université Clermont Auvergne, UMR 1071 Inserm, USC-INRAE 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), 63000, Clermont-Ferrand, France
| | - Sandrine Chalancon
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Ophélie Uriot
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Florence Van Herreweghen
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Tom Van de Wiele
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, INRAE, UMR 454 MEDIS, Microbiologie Environnement Digestif et Santé (MEDIS), CRNH Auvergne, 63000, Clermont-Ferrand, France.
| |
Collapse
|
35
|
Monk JM. Genome-scale metabolic network reconstructions of diverse Escherichia strains reveal strain-specific adaptations. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210236. [PMID: 35989599 PMCID: PMC9393557 DOI: 10.1098/rstb.2021.0236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Bottom-up approaches to systems biology rely on constructing a mechanistic basis for the biochemical and genetic processes that underlie cellular functions. Genome-scale network reconstructions of metabolism are built from all known metabolic reactions and metabolic genes in a target organism. A network reconstruction can be converted into a mathematical format and thus lend itself to mathematical analysis. Genome-scale models (GEMs) of metabolism enable a systems approach to characterize the pan and core metabolic capabilities of the Escherichia genus. In this work, GEMs were constructed for 222 representative strains of Escherichia across HC1100 levels spanning the known Escherichia phylogeny. The models were used to study Escherichia metabolic diversity and speciation on a large scale. The results show that unique strain-specific metabolic capabilities correspond to different species and nutrient niches. This work is a first step towards a curated reconstruction of pan-Escherichia metabolism. This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.
Collapse
Affiliation(s)
- Jonathan M Monk
- Department of Bioengineering, University of California, 9500 Gilman Drive, San Diego, La Jolla, CA 92093-0412, USA
| |
Collapse
|
36
|
Two modes of evolution shape bacterial strain diversity in the mammalian gut for thousands of generations. Nat Commun 2022; 13:5604. [PMID: 36153389 PMCID: PMC9509342 DOI: 10.1038/s41467-022-33412-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show how rapid ecotype formation and phage domestication can be in the mammalian gut. Here, the authors show that a colonizing bacterial strain evolves in the gut by either generating ecotypes or continuously fixing beneficial mutations. They associate the first mode to metabolic mutations and the second to domestication of bacteriophages that are incorporated into the bacterial genome.
Collapse
|
37
|
Latchmore T, Hynds PD, Stephen Brown R, McDermott K, Majury A. Estimating the duration and overlap of Escherichia coli contamination events in private groundwater supplies for quantitative risk assessment using a multiannual (2010-2017) provincial dataset. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119784. [PMID: 35843457 DOI: 10.1016/j.envpol.2022.119784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Approximately 1.6 million individuals in Ontario rely on private water wells. Private well water quality in Ontario remains the responsibility of the well owner, and due to the absence of regulation, quantitative microbial risk assessment (QMRA) likely represents the most effective approach to estimating and mitigating waterborne infection risk(s) from these supplies. Annual contamination duration (i.e., contaminated days per annum) represents a central input for waterborne QMRA; however, it is typically based on laboratory studies or meta-analyses, thus representing an important limitation for risk assessment, as groundwater mesocosms cannot accurately replicate subsurface conditions. The present study sought to address these limitations using a large spatio-temporal in-situ groundwater quality dataset (>700,000 samples) to evaluate aquifer-specific E. coli die-off rates (CFU/100 mL per day decline), subsequent contamination sequence duration(s) and the likelihood of overlapping contamination events. Findings indicate median E. coli die-off rates of 0.38 CFU/100 mL per day and 0.64 CFU/100 mL per day, for private wells located in unconsolidated and consolidated aquifers, respectlvely, with mean calculated contamination sequence durations of 18 days (unconsolidated) and 11 days (consolidated). Study findings support and permit development of increasingly evidence-based, regionally- and temporally-specific quantitative waterborne risk assessment.
Collapse
Affiliation(s)
- Tessa Latchmore
- School of Environmental Studies, Queen's University, 99 University Avenue, Kingston, Ontario, Canada
| | - Paul D Hynds
- Technological University Dublin, Park House, 191 N Circular Rd, Dublin, Ireland.
| | - R Stephen Brown
- School of Environmental Studies, Queen's University, 99 University Avenue, Kingston, Ontario, Canada
| | - Kevin McDermott
- Public Health Ontario, 181 Barrie Street, Kingston, Ontario, Canada
| | - Anna Majury
- School of Environmental Studies, Queen's University, 99 University Avenue, Kingston, Ontario, Canada; Public Health Ontario, 181 Barrie Street, Kingston, Ontario, Canada
| |
Collapse
|
38
|
Gambushe SM, Zishiri OT, El Zowalaty ME. Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective. Infect Drug Resist 2022; 15:4645-4673. [PMID: 36039321 PMCID: PMC9420067 DOI: 10.2147/idr.s365269] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.
Collapse
Affiliation(s)
- Sydney M Gambushe
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Oliver T Zishiri
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Mohamed E El Zowalaty
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75 123, Sweden
| |
Collapse
|
39
|
Behruznia M, Gordon DM. Molecular and metabolic characteristics of wastewater associated Escherichia coli strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:646-654. [PMID: 35638456 PMCID: PMC9543349 DOI: 10.1111/1758-2229.13076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/04/2023]
Abstract
We previously characterized the genetic diversity of Escherichia coli strains isolated from septic tanks in the Canberra region, Australia. In this study, we used repetitive element palindromic (REP) PCR fingerprinting to identify dominant REP-types belonging to phylogroups A and B1 strains across septic tanks. Subsequently, 76 E. coli strains were selected for whole-genome sequencing and phenotype microarrays. Comparative genome analysis was performed to compare septic tank E. coli genomes with a collection of 433 E. coli isolates from different hosts and freshwater. Clonal complexes (CCs) 10 (n = 15) and 399 (n = 10) along with sequence type (ST) 401 (n = 9) were the common lineages in septic tanks. CC10 strains have been detected from animal hosts and freshwater, whereas CC399 and ST401 strains appeared to be associated with septic tanks as they were uncommon in isolates from other sources. Comparative genome analysis revealed that CC399 and ST401 were genetically distinct from other isolates and carried an abundance of niche-specific traits involved in environmental adaptation. These strains also showed distinct metabolic characteristics, such as the ability to utilize pectin, which may provide a fitness advantage under nutrient-limited conditions. The results of this study characterized the adaptive mechanisms allowing E. coli to persist in wastewater.
Collapse
Affiliation(s)
- Mahboobeh Behruznia
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - David M. Gordon
- Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| |
Collapse
|
40
|
Arnauts K, Sudhakar P, Verstockt S, Lapierre C, Potche S, Caenepeel C, Verstockt B, Raes J, Vermeire S, Sabino J, Verfaillie C, Ferrante M. Microbiota, not host origin drives ex vivo intestinal epithelial responses. Gut Microbes 2022; 14:2089003. [PMID: 35758256 PMCID: PMC9235885 DOI: 10.1080/19490976.2022.2089003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Microbial dysbiosis is an established finding in patients with inflammatory bowel disease (IBD), but host-microbial interactions are poorly understood. We aimed to unravel the effect of microbiota exposure on intestinal epithelial cells. Confluent Transwell® organoid monolayers of eight UC patients and eight non-IBD controls were co-cultured for six hours with microbiota (3x108 cells) of UC patients or a healthy volunteer (HV), in the presence or absence of an inflammatory cytokine mix. Transepithelial electrical resistance (TEER), fluorescein isothiocyanate (FITC) dextran measurements, and RNA sequencing were performed on epithelial cells, and 16S rRNA sequencing on microbiota samples before and after co-culture. Transcriptomic response following microbiota exposure was not different between epithelial cells from UC patients or non-IBD controls. Following UC microbiota exposure, but not HV microbiota, a strong decrease in epithelial barrier integrity was observed in both UC and HV epithelial cells by TEER and FITC dextran measurements. Exposure of inflamed epithelium to UC microbiota induced transcriptomic stress pathways including activation of EGR1, MAPK and JAK/STAT signaling, as well as AP-1 family and FOSL transcripts. Stress responses after HV microbiota stimulation were milder. We conclude that not the epithelial cell origin (UC versus non-IBD) but the microbial donor drives transcriptomic responses, as exposure to UC microbiota was sufficient to induce stress responses in all epithelial cells. Further research on therapies to restore the microbial balance, to remove the constant trigger of dysbiosis, is required.
Collapse
Affiliation(s)
- Kaline Arnauts
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Development and Regeneration, Stem Cell Institute Leuven (SCIL), KU Leuven, Leuven, Belgium
| | - Padhmanand Sudhakar
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Sare Verstockt
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Cynthia Lapierre
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Selina Potche
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Clara Caenepeel
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - João Sabino
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute Leuven (SCIL), KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium,CONTACT Marc Ferrante Department of Gastroenterology and Hepatology University Hospitals Leuven, Herestraat 49, Leuven3000, Belgium
| |
Collapse
|
41
|
Dey P, Ray Chaudhuri S. Cancer-Associated Microbiota: From Mechanisms of Disease Causation to Microbiota-Centric Anti-Cancer Approaches. BIOLOGY 2022; 11:757. [PMID: 35625485 PMCID: PMC9138768 DOI: 10.3390/biology11050757] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/08/2022] [Accepted: 05/12/2022] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori infection is the only well-established bacterial cause of cancer. However, due to the integral role of tissue-resident commensals in maintaining tissue-specific immunometabolic homeostasis, accumulated evidence suggests that an imbalance of tissue-resident microbiota that are otherwise considered as commensals, can also promote various types of cancers. Therefore, the present review discusses compelling evidence linking tissue-resident microbiota (especially gut bacteria) with cancer initiation and progression. Experimental evidence supporting the cancer-causing role of gut commensal through the modulation of host-specific processes (e.g., bile acid metabolism, hormonal effects) or by direct DNA damage and toxicity has been discussed. The opportunistic role of commensal through pathoadaptive mutation and overcoming colonization resistance is discussed, and how chronic inflammation triggered by microbiota could be an intermediate in cancer-causing infections has been discussed. Finally, we discuss microbiota-centric strategies, including fecal microbiota transplantation, proven to be beneficial in preventing and treating cancers. Collectively, this review provides a comprehensive understanding of the role of tissue-resident microbiota, their cancer-promoting potentials, and how beneficial bacteria can be used against cancers.
Collapse
Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, India
| | - Saumya Ray Chaudhuri
- Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology, Chandigarh 160036, India;
| |
Collapse
|
42
|
Schmidt F, Zimmermann J, Tanna T, Farouni R, Conway T, Macpherson AJ, Platt RJ. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 2022; 376:eabm6038. [PMID: 35549411 PMCID: PMC11163514 DOI: 10.1126/science.abm6038] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.
Collapse
Affiliation(s)
- Florian Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Jakob Zimmermann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Tanmay Tanna
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Department of Computer Science, ETH Zurich, Universitätstrasse 6, 8092 Zurich, Switzerland
| | - Rick Farouni
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Tyrrell Conway
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Andrew J. Macpherson
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Switzerland
- Department for Biomedical Research, University of Bern, Bern, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Randall J. Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland
- Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| |
Collapse
|
43
|
Foster-Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev 2022; 46:fuac008. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
| |
Collapse
|
44
|
Abstract
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to establish within the ecosystem. However, the complicated network of interactions between elements of the intestinal environment makes it challenging to uncover emergent properties of the system using only reductionist methods. A systems biology approach, which aims to investigate complex systems by examining the behavior and relationships of all elements of the system, may afford a more holistic perspective of the colonization process. Here, we examine the confluence between the gut landscape and bacterial colonization through the lens of systems biology. We offer an overview of the conceptual and methodological underpinnings of systems biology, followed by a discussion of key elements of the gut ecosystem as they pertain to bacterial establishment and growth. We conclude by reintegrating these elements to guide future comprehensive investigations of the ecosystem in the context of bacterial intestinal colonization.
Collapse
Affiliation(s)
- Madeline R. Barron
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
45
|
Sy BM, Tree JJ. The Small RNA CyaR Activates Translation of the Outer Membrane Haem Receptor chuA in Enterohemorrhagic Escherichia coli. Front Microbiol 2022; 13:821196. [PMID: 35422774 PMCID: PMC9002310 DOI: 10.3389/fmicb.2022.821196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/10/2022] [Indexed: 12/22/2022] Open
Abstract
To sense the transition from environment to host, bacteria use a range of environmental cues to control expression of virulence genes. Iron is tightly sequestered in host tissues and in the human pathogen enterohemorrhagic Escherichia coli (EHEC) iron-limitation induces transcription of the outer membrane haem transporter encoded by chuAS. ChuA expression is post-transcriptionally activated at 37°C by a FourU RNA thermometer ensuring that the haem receptor is only expressed under low iron, high temperature conditions that indicate the host. Here we demonstrate that expression of chuA is also independently regulated by the cAMP-responsive small RNA (sRNA) CyaR and transcriptional terminator Rho. These results indicate that chuAS expression is regulated at the transcription initiation, transcript elongation, and translational level. We speculate that additional sensing of the gluconeogenic environment allows further precision in determining when EHEC is at the gastrointestinal epithelium of the host. With previous studies, it appears that the chuAS transcript is controlled by eight regulatory inputs that control expression through six different transcriptional and post-transcriptional mechanisms. The results highlight the ability of regulatory sRNAs to integrate multiple environmental signals into a layered hierarchy of signal input.
Collapse
Affiliation(s)
- Brandon M Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| |
Collapse
|
46
|
Hu J, Zhong X, Liu Y, Yan J, Zhou D, Qin D, Xiao X, Zheng Y, Wen L, Tan R, Liang P, Liu Y. Correlation between intestinal flora disruption and protein–energy wasting in patients with end-stage renal disease. BMC Nephrol 2022; 23:130. [PMID: 35369865 PMCID: PMC8978364 DOI: 10.1186/s12882-022-02762-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 03/23/2022] [Indexed: 01/14/2023] Open
Abstract
Background Different dialysis treatments may affect the composition and structure of the intestinal flora of dialysis-treated chronic kidney disease (CKD) patients. This study aimed to analyze the correlations between the different flora and the nutritional indexes and further explore the potential metabolic pathways in patients with CKD in end-stage renal disease (ESRD). Methods Altogether, 102 patients with ESRD were recruited and categorized into the hemodialysis (HD) group (N = 49) and the peritoneal dialysis (PD) group (N = 53). Their biochemical indexes, anthropometric indicators, and inflammatory markers were determined. The total genomic DNA was extracted for 16S ribosomal DNA sequencing. Furthermore, bioinformatics analysis was employed for functional analysis. Results Anthropometric indicators, including handgrip strength, mid-upper arm circumference, mid-upper arm muscle circumference, and body mass index, in the HD and PD groups showed a positive correlation with butyric acid-producing bacteria (Rosella and Phascolarctobacterium) and a negative correlation with conditional pathogens (Escherichia spp.). Meanwhile, the inflammatory markers, including high-sensitivity C-reactive protein and interleukin-6, were significantly higher in the PD-protein–energy wasting (PEW) group than in the PD-non-protein–energy wasting (NPEW) group; although they showed an increasing trend in the HD-PEW group, no significant difference was noted. Rosella was considerably scarce in the HD-PEW group than in the HD-NPEW group, whereas Escherichia was substantially more abundant in the PD-PEW group than in the PD-NPEW group. Compared with the HD group, the essential amino acid synthesis pathway, amino acid metabolism-related enzyme pathways, and aminoacyl-transfer RNA biosynthesis pathways were weakened in the PD group. Most carbohydrate metabolic pathways were weakened, although the tricarboxylic acid cycle was slightly enhanced. Concurrently, the fatty acid metabolism was enhanced, whereas fatty acid synthesis was weakened; the metabolic pathways of B vitamins were also weakened. These potential metabolic pathways of the various compounds released by intestinal flora showed a significant correlation with blood biochemical indexes, anthropometric indicators, and inflammatory markers. Conclusion In patients with ESRD, different dialysis treatments affected the abundance of butyric acid-producing bacteria (Rosella and Phascolarctobacterium) and conditional pathogens (Escherichia spp.). Butyric acid-producing bacteria showed a positive correlation with PEW and showed a negative correlation with Escherichia. Improving the intestinal diversity and increasing the amount of butyric acid-producing bacteria, such as Blautella, Faecococcus, and Phascolarctobacterium, are potential therapeutic approaches to enhance protein–energy consumption in patients with ESRD.
Collapse
|
47
|
Metcalfe GD, Sargent F, Hippler M. Hydrogen production in the presence of oxygen by Escherichia coli K-12. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35343886 PMCID: PMC9558352 DOI: 10.1099/mic.0.001167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Escherichia coli is a facultative anaerobe that can grow in a variety of environmental conditions. In the complete absence of O2, E. coli can perform a mixed-acid fermentation that contains within it an elaborate metabolism of formic acid. In this study, we use cavity-enhanced Raman spectroscopy (CERS), FTIR, liquid Raman spectroscopy, isotopic labelling and molecular genetics to make advances in the understanding of bacterial formate and H2 metabolism. It is shown that, under anaerobic (anoxic) conditions, formic acid is generated endogenously, excreted briefly from the cell, and then taken up again to be disproportionated to H2 and CO2 by formate hydrogenlyase (FHL-1). However, exogenously added D-labelled formate behaves quite differently from the endogenous formate and is taken up immediately, independently, and possibly by a different mechanism, by the cell and converted to H2 and CO2. Our data support an anion-proton symport model for formic acid transport. In addition, when E. coli was grown in a micro-aerobic (micro-oxic) environment it was possible to analyse aspects of formate and O2 respiration occurring alongside anaerobic metabolism. While cells growing under micro-aerobic conditions generated endogenous formic acid, no H2 was produced. However, addition of exogenous formate at the outset of cell growth did induce FHL-1 biosynthesis and resulted in formate-dependent H2 production in the presence of O2.
Collapse
Affiliation(s)
- George D Metcalfe
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Frank Sargent
- School of Natural & Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael Hippler
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| |
Collapse
|
48
|
Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe 2022; 30:183-199.e10. [PMID: 35085504 DOI: 10.1016/j.chom.2022.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet causes microbiota imbalances that underlay many pathological conditions (i.e., dysbiosis). Although the effects of dietary changes on microbiota composition and functions are well documented, their impact in gut bacterial evolution remains unexplored. We followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly in the gut and Western-style diet selected for mutations that promote degradation of mucin-derived glycans. Periodic dietary changes caused fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intraspecies genetic diversity compared to constant dietary regimens. These results show that dietary changes leave a genetic signature in microbiome members and suggest that B. thetaiotaomicron genetic diversity could be a biomarker for dietary differences among individuals.
Collapse
|
49
|
Zhen W, Liu Y, Shao Y, Ma Y, Wu Y, Guo F, Abbas W, Guo Y, Wang Z. Yeast β-Glucan Altered Intestinal Microbiome and Metabolome in Older Hens. Front Microbiol 2022; 12:766878. [PMID: 34975793 PMCID: PMC8718749 DOI: 10.3389/fmicb.2021.766878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 12/31/2022] Open
Abstract
The prebiotics- and probiotics-mediated positive modulation of the gut microbiota composition is considered a useful approach to improve gut health and food safety in chickens. This study explored the effects of yeast β-glucan (YG) supplementation on intestinal microbiome and metabolites profiles as well as mucosal immunity in older hens. A total of 256 43-week-old hens were randomly assigned to two treatments, with 0 and 200 mg/kg of YG. Results revealed YG-induced downregulation of toll-like receptors (TLRs) and cytokine gene expression in the ileum without any effect on the intestinal barrier. 16S rRNA analysis claimed that YG altered α- and β-diversity and enriched the relative abundance of class Bacilli, orders Lactobacillales and Enterobacteriales, families Lactobacillaceae and Enterobacteriaceae, genera Lactobacillus and Escherichia–Shigella, and species uncultured bacterium-Lactobacillus. Significant downregulation of cutin and suberin, wax biosynthesis, atrazine degradation, vitamin B6 metabolism, phosphotransferase system (PTS), steroid degradation, biosynthesis of unsaturated fatty acids, aminobenzoate degradation and quorum sensing and upregulation of ascorbate and aldarate metabolism, C5-branched dibasic acid metabolism, glyoxylate and dicarboxylate metabolism, pentose and glucuronate interconversions, steroid biosynthesis, carotenoid biosynthesis, porphyrin and chlorophyll metabolism, sesquiterpenoid and triterpenoid biosynthesis, lysine degradation, and ubiquinone and other terpenoid-quinone biosyntheses were observed in YG-treated hens, as substantiated by the findings of untargeted metabolomics analysis. Overall, YG manifests prebiotic properties by altering gut microbiome and metabolite profiles and can downregulate the intestinal mucosal immune response of breeder hens.
Collapse
Affiliation(s)
- Wenrui Zhen
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.,State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuchen Liu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yujing Shao
- College of Biology, China Agricultural University, Beijing, China
| | - Yanbo Ma
- Henan International Joint Laboratory of Animal Welfare and Health Breeding, College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Yuanyuan Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fangshen Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Waseem Abbas
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhong Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
50
|
Zhang H, Mu X, Wang H, Wang H, Wang H, Li Y, Mu Y, Song J, Xia L. Lacticaseibacillus casei ATCC 393 Cannot Colonize the Gastrointestinal Tract of Crucian Carp. Microorganisms 2021; 9:microorganisms9122547. [PMID: 34946147 PMCID: PMC8708626 DOI: 10.3390/microorganisms9122547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 11/25/2022] Open
Abstract
Lactic acid bacteria (LAB) are commonly applied to fish as a means of growth promotion and disease prevention. However, evidence regarding whether LAB colonize the gastrointestinal (GI) tract of fish remains sparse and controversial. Here, we investigated whether Lacticaseibacillus casei ATCC 393 (Lc) can colonize the GI tract of crucian carp. Sterile feed irradiated with 60Co was used to eliminate the influence of microbes, and 100% rearing water was renewed at 5-day intervals to reduce the fecal–oral circulation of microbes. The experiment lasted 47 days and was divided into three stages: the baseline period (21 days), the administration period (7 days: day −6 to 0) and the post-administration period (day 1 to 19). Control groups were fed a sterile basal diet during the whole experimental period, whereas treatment groups were fed with a mixed diet containing Lc (1 × 107 cfu/g) and spore of Geobacillus stearothermophilus (Gs, 1 × 107 cfu/g) during the administration period and a sterile basal diet during the baseline and post-administration periods. An improved and highly sensitive selective culture method (SCM) was employed in combination with a transit marker (a Gs spore) to monitor the elimination of Lc in the GI tract. The results showed that Lc (<2 cfu/gastrointestine) could not be detected in any of the fish sampled from the treatment group 7 days after the cessation of the mixed diet, whereas Gs could still be detected in seven out of nine fish at day 11 and could not be detected at all at day 15. Therefore, the elimination speed of Lc was faster than that of the transit marker. Furthermore, high-throughput sequencing analysis combined with SCM was used to reconfirm the elimination kinetics of Lc in the GI tract. The results show that the Lc in the crucian carp GI tract, despite being retained at low relative abundance from day 7 (0.11% ± 0.03%) to 21, was not viable. The experiments indicate that Lc ATCC 393 cannot colonize the GI tract of crucian carp, and the improved selective culture in combination with a transit marker represents a good method for studying LAB colonization of fish.
Collapse
Affiliation(s)
- Hongyu Zhang
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, China; (H.Z.); (X.M.); (H.W.); (H.W.); (Y.L.)
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Xiyan Mu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, China; (H.Z.); (X.M.); (H.W.); (H.W.); (Y.L.)
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Hongwei Wang
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Haibo Wang
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, China; (H.Z.); (X.M.); (H.W.); (H.W.); (Y.L.)
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Hui Wang
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, China; (H.Z.); (X.M.); (H.W.); (H.W.); (Y.L.)
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Yingren Li
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing 100141, China; (H.Z.); (X.M.); (H.W.); (H.W.); (Y.L.)
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
| | - Yingchun Mu
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
- Key Laboratory of Control of Quality and Safety for Aquatic Products (Ministry of Agriculture and Rural Affairs), Chinese Academy of Fishery Sciences, Beijing 100141, China
- Correspondence: (Y.M.); (J.S.); (L.X.)
| | - Jinlong Song
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
- Key Laboratory of Control of Quality and Safety for Aquatic Products (Ministry of Agriculture and Rural Affairs), Chinese Academy of Fishery Sciences, Beijing 100141, China
- Correspondence: (Y.M.); (J.S.); (L.X.)
| | - Lei Xia
- Chinese Academy of Fishery Sciences, Beijing 100141, China;
- Correspondence: (Y.M.); (J.S.); (L.X.)
| |
Collapse
|