1
|
De Vrieze J, De Mulder T, Matassa S, Zhou J, Angenent LT, Boon N, Verstraete W. Stochasticity in microbiology: managing unpredictability to reach the Sustainable Development Goals. Microb Biotechnol 2020; 13:829-843. [PMID: 32311222 PMCID: PMC7264747 DOI: 10.1111/1751-7915.13575] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023] Open
Abstract
Pure (single) cultures of microorganisms and mixed microbial communities (microbiomes) have been important for centuries in providing renewable energy, clean water and food products to human society and will continue to play a crucial role to pursue the Sustainable Development Goals. To use microorganisms effectively, microbial engineered processes require adequate control. Microbial communities are shaped by manageable deterministic processes, but also by stochastic processes, which can promote unforeseeable variations and adaptations. Here, we highlight the impact of stochasticity in single culture and microbiome engineering. First, we discuss the concepts and mechanisms of stochasticity in relation to microbial ecology of single cultures and microbiomes. Second, we discuss the consequences of stochasticity in relation to process performance and human health, which are reflected in key disadvantages and important opportunities. Third, we propose a suitable decision tool to deal with stochasticity in which monitoring of stochasticity and setting the boundaries of stochasticity by regulators are central aspects. Stochasticity may give rise to some risks, such as the presence of pathogens in microbiomes. We argue here that by taking the necessary precautions and through clever monitoring and interpretation, these risks can be mitigated.
Collapse
Affiliation(s)
- Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | | | - Silvio Matassa
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, via Claudio 21, 80125, Naples, Italy
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Largus T Angenent
- Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Willy Verstraete
- Center for Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Gent, Belgium
- Avecom NV, Industrieweg 122P, Wondelgem, 9032, Belgium
| |
Collapse
|
2
|
Van der Heyden C, De Mulder T, Volcke EIP, Demeyer P, Heyndrickx M, Rasschaert G. Long-term microbial community dynamics at two full-scale biotrickling filters treating pig house exhaust air. Microb Biotechnol 2019; 12:775-786. [PMID: 31106964 PMCID: PMC6559015 DOI: 10.1111/1751-7915.13417] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/23/2019] [Accepted: 04/06/2019] [Indexed: 11/30/2022] Open
Abstract
In this study, the microbial community structure of two full‐scale biotrickling filters treating exhaust air from a pig housing facility were evaluated using 16S metabarcoding. The effect of inoculation with activated sludge of a nearby domestic waste water treatment plant was investigated, which is a cheap procedure and easy to apply in practice. The study was performed at a three‐stage and a two‐stage full‐scale biotrickling filter; of which, only the latter was inoculated. Both biotrickling filters evolved towards a rather similar community over time, which differed from the one in the activated sludge used for inoculation. However, the bacterial population at both biotrickling filters showed small differences on the family level. A large population of heterotrophic bacteria, including denitrifying bacteria, was present in both biotrickling filters. In the non‐inoculated biotrickling filter, nitrite‐oxidizing bacteria (NOB) could not be detected, which corresponded with the incomplete nitrification leading to high nitrite accumulation observed in this system. Inoculation with the wide spectrum inoculum activated sludge had in this study a positive effect on the biotrickling filter performance (higher ammonia removal and lower nitrous oxide production). It could thus be beneficial to inoculate biotrickling filters in order to enrich NOB at the start‐up, making it easier to keep the free nitrous acid concentration low enough to not be inhibited by it.
Collapse
Affiliation(s)
- Caroline Van der Heyden
- Department of Biosystems Engineering, Ghent University, Coupure links 653, 9000, Gent, Belgium.,Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 115, bus 1, 9820, Merelbeke, Belgium.,Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Thijs De Mulder
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Eveline I P Volcke
- Department of Biosystems Engineering, Ghent University, Coupure links 653, 9000, Gent, Belgium
| | - Peter Demeyer
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 115, bus 1, 9820, Merelbeke, Belgium
| | - Marc Heyndrickx
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium.,Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Geertui Rasschaert
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| |
Collapse
|
3
|
De Mulder T, Rasschaert G, Van Coillie E, Van den Meersche T, Haegeman A, Ruttink T, de Wiele TV, Heyndrickx M. Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig's Cecum. Microb Drug Resist 2018; 25:304-315. [PMID: 30234420 DOI: 10.1089/mdr.2018.0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes. RESULTS The effect of three concentrations DOX were tested; 1 and 4 mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16 mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1 mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4 mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4 mg/L DOX. Only 16 mg/L DOX caused minor enrichments. CONCLUSIONS Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.
Collapse
Affiliation(s)
- Thijs De Mulder
- 1 Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO) , Melle, Belgium .,2 Center for Microbial Ecology and Technology (Cmet), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University , Ghent, Belgium
| | - Geertrui Rasschaert
- 1 Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO) , Melle, Belgium
| | - Els Van Coillie
- 1 Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO) , Melle, Belgium
| | - Tina Van den Meersche
- 1 Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO) , Melle, Belgium .,3 Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Merelbeke, Belgium
| | - Annelies Haegeman
- 4 Plant Sciences Unit, Institute for Agriculture and Fisheries Research (ILVO) , Melle, Belgium
| | - Tom Ruttink
- 4 Plant Sciences Unit, Institute for Agriculture and Fisheries Research (ILVO) , Melle, Belgium
| | - Tom Van de Wiele
- 2 Center for Microbial Ecology and Technology (Cmet), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University , Ghent, Belgium
| | - Marc Heyndrickx
- 1 Technology and Food Science Unit, Institute for Agricultural and Fisheries Research (ILVO) , Melle, Belgium .,3 Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University , Merelbeke, Belgium
| |
Collapse
|
4
|
De Mulder T, Peiren N, Vandaele L, Ruttink T, De Campeneere S, Van de Wiele T, Goossens K. Impact of breed on the rumen microbial community composition and methane emission of Holstein Friesian and Belgian Blue heifers. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
De Mulder T, Goossens K, Peiren N, Vandaele L, Haegeman A, De Tender C, Ruttink T, de Wiele TV, De Campeneere S. Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural. FEMS Microbiol Ecol 2017; 93:fiw251. [PMID: 28011597 DOI: 10.1093/femsec/fiw251] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2016] [Indexed: 11/13/2022] Open
Abstract
The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid-adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid-adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep). The bacterial and methanogen communities of these sample types were analysed using 16S metabarcoding and qPCR. The results indicate that the liquid and solid-adherent environments are distinguished mainly by the differential abundance of specific taxonomic groups. Cellulolytic bacteria that pioneer biofilm formation, together with secondary colonisers are prevalent in solid-adherent samples, while dominant species in the fluid samples are primarily identified as consumers of soluble nutrients. Also, methanogen species are found to have a preference for either a solid-adherent or free-living occurrence. The epimural environment is characterised by a different microbial profile. Ten bacterial families and two methanogen genera are almost exclusively found in this environment.
Collapse
Affiliation(s)
- Thijs De Mulder
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Karen Goossens
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Nico Peiren
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Leen Vandaele
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| | - Annelies Haegeman
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Caroline De Tender
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Tom Ruttink
- Institute for Agriculture and Fisheries Research (ILVO), Plant Science Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure 653, 9000 Ghent, Belgium
| | - Sam De Campeneere
- Institute for Agriculture and Fisheries Research (ILVO), Animal Science Unit, Scheldeweg 68, 9090 Melle, Belgium
| |
Collapse
|
6
|
Daeseleire E, De Graef E, Rasschaert G, De Mulder T, Van den Meersche T, Van Coillie E, Dewulf J, Heyndrickx M. Antibiotic use and resistance in animals: Belgian initiatives. Drug Test Anal 2017; 8:549-55. [PMID: 27443210 DOI: 10.1002/dta.2010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 02/25/2016] [Accepted: 04/07/2016] [Indexed: 11/06/2022]
Abstract
The widespread use of antibiotics in animals is causing concerns about the growing risk for development and the spread of antibiotic-resistant bacteria. Antibiotic consumption is higher in animals than in humans as reported in a joint publication of EFSA (European Food Safety Agency), ECDC (European Centre for Disease Prevention and Control), and EMA (European Medicines Agency) using data from 2011 and 2012. Both in humans and animals, positive associations between the consumption of antibiotics and resistant bacteria are observed. Responsible use of antibiotics in humans and animals should therefore be promoted. In this paper some general aspects of antibiotic resistance such as microbiological versus clinical resistance, intrinsic versus acquired resistance, resistance mechanisms, and transfer of resistance are briefly introduced. In 2012, the Belgian Center of Expertise on Antimicrobial Consumption and Resistance in Animals (AMCRA) was founded. Its mission is to collect and analyze all data related to antibiotic use and resistance in animals in Belgium and to communicate these findings in a neutral and objective manner. One of AMCRA's 10 objectives is a 50% reduction in antibiotic consumption in veterinary medicine in Belgium by 2020. The aim of this paper is to report on the achievements of this national project. The Institute for Agricultural and Fisheries Research (ILVO, Merelbeke-Melle), in collaboration with Ghent University, is currently working on three nationally funded projects on antibiotic resistance in animal husbandry. In the first project, an in vitro model is used to study the influence of low antibiotic concentrations due to carry-over after production and usage of medicated feed on the development of resistance in the pig gut. Part of that project is to develop a quantitative risk assessment model. A second project focuses on tracking excreted antibiotics used in pig rearing and their influence on the development of antibiotic resistance in pig manure and the environment. In the last project, the relation between the use of biocides in animal husbandry and antibiotic resistance development are being studied. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Els Daeseleire
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Evelyne De Graef
- Center of Expertise on Antimicrobial Consumption and Resistance in Animals (AMCRA), Eurostation II, Victor Hortaplein 40 bus 10, 1060, Brussels, Belgium.,Ghent University, Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Geertrui Rasschaert
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Thijs De Mulder
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Tina Van den Meersche
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium.,Ghent University, Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Els Van Coillie
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium
| | - Jeroen Dewulf
- Ghent University, Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Marc Heyndrickx
- Institute for Agricultural and Fisheries Research (ILVO), Brusselsesteenweg 370, 9090, Melle, Belgium.,Ghent University, Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Salisburylaan 133, 9820, Merelbeke, Belgium
| |
Collapse
|