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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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2
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Liu X, Pollner B, Paulitsch-Fuchs AH, Fuchs EC, Dyer NP, Loiskandl W, Lass-Flörl C. Investigation of the effect of sustainable magnetic treatment on the microbiological communities in drinking water. ENVIRONMENTAL RESEARCH 2022; 213:113638. [PMID: 35705130 DOI: 10.1016/j.envres.2022.113638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
The drinking water scarcity is posing a threat to mankind, hence better water quality management methods are required. Magnetic water treatment, which has been reported to improve aesthetic water quality and reduce scaling problems, can be an important addition to the traditional disinfectant dependent treatment. Despite the extensive market application opportunities, the effect of magnetic fields on (microbial) drinking water communities and subsequently the biostability is still largely unexplored, although the first patent was registered already 1945. Here flow cytometry was applied to assess the effect of weak magnetic fields (≤10 G) with strong gradients (≈800 G/m) on drinking water microbial communities. Drinking water was collected from the tap and placed inside the magnetic field (treated) and 5 m away from the magnet to avoid any background interferences (control) using both a static set-up and a shaking set-up. Samples were collected during a seven-day period for flow cytometry examination. Additionally, the effects of magnetic fields on the growth of Pseudomonas aeruginosa in autoclaved tap water were examined. Based on the fluorescent intensity of the stained nucleic acid content, the microbial cells were grouped into low nucleic acid content (LNA) and high nucleic acid content (HNA). Our results show that the LNA was dominant under nutrient limited condition while the HNA dominates when nutrient is more available. Such behavior of LNA and HNA matches well with the long discussed r/K selection model where r-strategists adapted to eutrophic conditions and K-strategists adapted to oligotrophic conditions. The applied magnetic fields selectively promote the growth of LNA under nutrient rich environment, which indicates a beneficial effect on biostability enhancement. Inhibition on an HNA representative Pseudomonas aeruginosa has also been observed. Based on our laboratory observations, we conclude that magnetic field treatment can be a sustainable method for microbial community management with great potential.
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Affiliation(s)
- Xiaoxia Liu
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bernhard Pollner
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Astrid H Paulitsch-Fuchs
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 2, 8010, Graz, Austria; Carinthia University of Applied Sciences, Biomedical Science, St. Veiterstraße 47, 9020 Klagenfurt, Austria
| | - Elmar C Fuchs
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Optical Sciences Group, Faculty of Science and Technology (TNW), University of Twente, Drienerlolaan 5, 7522NB Enschede, the Netherlands.
| | - Nigel P Dyer
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Coherent Water Systems, 2 Crich Avenue, DE23 6ES Derby, United Kingdom
| | - Willibald Loiskandl
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cornelia Lass-Flörl
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
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Verstraete W, Yanuka‐Golub K, Driesen N, De Vrieze J. Engineering microbial technologies for environmental sustainability: choices to make. Microb Biotechnol 2022; 15:215-227. [PMID: 34875143 PMCID: PMC8719809 DOI: 10.1111/1751-7915.13986] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 11/27/2022] Open
Abstract
Microbial technologies have provided solutions to key challenges in our daily lives for over a century. In the debate about the ongoing climate change and the need for planetary sustainability, microbial ecology and microbial technologies are rarely considered. Nonetheless, they can bring forward vital solutions to decrease and even prevent long-term effects of climate change. The key to the success of microbial technologies is an effective, target-oriented microbiome management. Here, we highlight how microbial technologies can play a key role in both natural, i.e. soils and aquatic ecosystems, and semi-natural or even entirely human-made, engineered ecosystems, e.g. (waste) water treatment and bodily systems. First, we set forward fundamental guidelines for effective soil microbial resource management, especially with respect to nutrient loss and greenhouse gas abatement. Next, we focus on closing the water circle, integrating resource recovery. We also address the essential interaction of the human and animal host with their respective microbiomes. Finally, we set forward some key future potentials, such as microbial protein and the need to overcome microphobia for microbial products and services. Overall, we conclude that by relying on the wisdom of the past, we can tackle the challenges of our current era through microbial technologies.
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Affiliation(s)
- Willy Verstraete
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
- Avecom NVIndustrieweg 122PWondelgem9032Belgium
| | - Keren Yanuka‐Golub
- The Institute of Applied ResearchThe Galilee SocietyP.O. Box 437Shefa‐AmrIsrael
| | | | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET)Faculty of Bioscience EngineeringGhent UniversityCoupure Links 653GentB‐9000Belgium
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Conversion of Carbon Monoxide to Chemicals Using Microbial Consortia. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 180:373-407. [PMID: 34811579 DOI: 10.1007/10_2021_180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Syngas, a gaseous mixture of CO, H2 and CO2, can be produced by gasification of carbon-containing materials, including organic waste materials or lignocellulosic biomass. The conversion of bio-based syngas to chemicals is foreseen as an important process in circular bioeconomy. Carbon monoxide is also produced as a waste gas in many industrial sectors (e.g., chemical, energy, steel). Often, the purity level of bio-based syngas and waste gases is low and/or the ratios of syngas components are not adequate for chemical conversion (e.g., by Fischer-Tropsch). Microbes are robust catalysts to transform impure syngas into a broad spectrum of products. Fermentation of CO-rich waste gases to ethanol has reached commercial scale (by axenic cultures of Clostridium species), but production of other chemical building blocks is underexplored. Currently, genetic engineering of carboxydotrophic acetogens is applied to increase the portfolio of products from syngas/CO, but the limited energy metabolism of these microbes limits product yields and applications (for example, only products requiring low levels of ATP for synthesis can be produced). An alternative approach is to explore microbial consortia, including open mixed cultures and synthetic co-cultures, to create a metabolic network based on CO conversion that can yield products such as medium-chain carboxylic acids, higher alcohols and other added-value chemicals.
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Fernandez-Gonzalez N, Braz GHR, Regueiro L, Lema JM, Carballa M. Microbial invasions in sludge anaerobic digesters. Appl Microbiol Biotechnol 2020; 105:21-33. [PMID: 33205286 DOI: 10.1007/s00253-020-11009-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/31/2020] [Accepted: 11/08/2020] [Indexed: 12/13/2022]
Abstract
Among processes that control microbial community assembly, microbial invasion has received little attention until recently, especially in the field of anaerobic digestion. However, knowledge of the principles regulating the taxonomic and functional stability of microbial communities is key to truly develop better predictive models and effective management strategies for the anaerobic digestion process. To date, available studies focus on microbial invasions in digesters feed with activated sludge from municipal wastewater treatment plants. Herein, this review summarizes the importance of invasions for anaerobic digestion management, the ecological theories about microbial invasions, the traits of activated sludge microorganisms entering the digesters, and the resident communities of anaerobic reactors that are relevant for invasions and the current knowledge about the success and impacts of invasions, and discusses the research needs on this topic. The initial data indicate that the impact of invasions is low and only a small percentage of the mostly aerobic microorganisms present in the activated sludge feed are able to become stablished in the anaerobic digesters. However, there are still numerous unknowns about microbial invasions in anaerobic digestion including the influence of anaerobic feedstocks or process perturbances that new approaches on microbial ecology could unveil. KEY POINTS: • Microbial invasions are key processes to develop better strategies for digesters management. • Knowledge on pathogen invasions can improve anaerobic digestion microbial safety. • To date, the number of successful invasions on anaerobic digesters from activated sludge organisms is low. • Feed organisms detected in digesters are mostly inactive residual populations. • Need to expand the range of invaders and operational scenarios studied.
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Affiliation(s)
- Nuria Fernandez-Gonzalez
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,Institute of Sustainable Processes, University of Valladolid, Valladolid, Spain.
| | - G H R Braz
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.,, Ribeirão Preto, Brazil
| | | | - J M Lema
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - M Carballa
- Department of Chemical Engineering, CRETUS Institute, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Peces M, Astals S, Jensen PD, Clarke WP. Transition of microbial communities and degradation pathways in anaerobic digestion at decreasing retention time. N Biotechnol 2020; 60:52-61. [PMID: 32858258 DOI: 10.1016/j.nbt.2020.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 01/04/2023]
Abstract
Tuning of operational variables is a common practice to control the anaerobic digestion process and, in advanced applications, to promote the accumulation of fermentation products. However, process variables are interrelated. In this study, the hydraulic retention time (HRT) was decoupled from the organic loading rate (OLR) in order to isolate the effect of HRT as a selective pressure on: process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and the microbial community. Four mesophilic anaerobic digesters were subjected to a sequential decrease in HRT from 15 to 8, 4 and 2 days while keeping the OLR constant at chemical oxygen demand of 1 gCOD L r-1 d-1. The results showed that HRT alone was insufficient to washout methanogens from the digesters, which in turn prevented the accumulation of volatile fatty acids (VFA). Methanosaeta was the dominant genus in the four digesters at all HRTs. Metabolic rates showed that process performance was controlled by hydrolysis, with a clear shift in acetogenic rates, from butyrate and propionate degradation to ethanol degradation at 4 and 2d HRT. The change in acetogenic pathways was attributed to a shift in the fermentation pathways co-current with changes in fermentative bacteria. At 2d HRT, biofilm was formed on the walls and paddles of the digesters, probably as a survival strategy. Most of the taxa in the biofilm were also present in the digester media. Overall, it is the combination of HRT with other operational parameters which promotes the washout of methanogens and the accumulation of VFA.
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Affiliation(s)
- Miriam Peces
- Centre for Solid Waste Bioprocessing, Schools of Civil and Chemical Engineering, The University of Queensland, St. Lucia, 4072, QLD, Australia; Department of Chemistry and Bioscience, Centre for Microbial Communities, Aalborg University, 9220 Aalborg, Denmark.
| | - Sergi Astals
- Advanced Water Management Centre, The University of Queensland, St Lucia, 4072, QLD, Australia; Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Paul D Jensen
- Advanced Water Management Centre, The University of Queensland, St Lucia, 4072, QLD, Australia
| | - William P Clarke
- Centre for Solid Waste Bioprocessing, Schools of Civil and Chemical Engineering, The University of Queensland, St. Lucia, 4072, QLD, Australia
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Feedstock thermal pretreatment selectively steers process stability during the anaerobic digestion of waste activated sludge. Appl Microbiol Biotechnol 2020; 104:3675-3686. [DOI: 10.1007/s00253-020-10472-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 10/24/2022]
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Zamorano-López N, Borrás L, Seco A, Aguado D. Unveiling microbial structures during raw microalgae digestion and co-digestion with primary sludge to produce biogas using semi-continuous AnMBR systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134365. [PMID: 31677459 DOI: 10.1016/j.scitotenv.2019.134365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/07/2019] [Accepted: 09/07/2019] [Indexed: 06/10/2023]
Abstract
Methane production from microalgae can be enhanced through anaerobic co-digestion with carbon-rich substrates and thus mitigate the inhibition risk associated with its low C:N ratio. Acclimated microbial communities for microalgae disruption can be used as a source of natural enzymes in bioenergy production. However, co-substrates with a certain microbial diversity such as primary sludge might shift the microbial structure. Substrates were generated in a Water Resource Recovery Facility (WRRF) and combined as follows: Scenedesmus or Chlorella digestion and microalgae co-digestion with primary sludge. The study was performed using two lab-scale Anaerobic Membrane Bioreactors (AnMBR). During three years, different feedstocks scenarios for methane production were evaluated with a special focus on the microbial diversity of the AnMBR. 57% of the population was shared between the different feedstock scenarios, revealing the importance of Anaerolineaceae members besides Smithella and Methanosaeta genera. The addition of primary sludge enhanced the microbial diversity of the system during both Chlorella and Scenedesmus co-digestion and promoted different microbial structures. Aceticlastic methanogen Methanosaeta was dominant in all the feedstock scenarios. A more remarkable role of syntrophic fatty acid degraders (Smithella, Syntrophobacteraceae) was observed during co-digestion when only microalgae were digested. However, no significant changes were observed in the microbial composition during anaerobic microalgae digestion when feeding only Chlorella or Scenedesmus. This is the first work revealing the composition of complex communities for semi-continuous bioenergy production from WRRF streams. The stability and maintenance of a microbial core over-time in semi-continuous AnMBRs is here shown supporting their future application in full-scale systems for raw microalgae digestion or co-digestion.
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Affiliation(s)
- N Zamorano-López
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain.
| | - L Borrás
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain.
| | - A Seco
- CALAGUA - Unidad Mixta UV-UPV, Departament d'Enginyeria Química, Universitat de València, Avinguda de la Universitat s/n, 46100 Burjassot, Valencia, Spain.
| | - D Aguado
- CALAGUA - Unidad Mixta UV-UPV, Institut Universitari d'Investigació d'Enginyeria de l'Aigua i Medi Ambient - IIAMA, Universitat Politècnica de Valencia, Camí de Vera s/n, 46022, Valencia, Spain.
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Abstract
After nearly two decades of subsidized and energy crop-oriented development, agricultural biogas production in Germany is standing at a crossroads. Fundamental challenges need to be met. In this article we sketch a vision of a future agricultural biogas plant that is an integral part of the circular bioeconomy and works mainly on the base of residues. It is flexible with regard to feedstocks, digester operation, microbial communities and biogas output. It is modular in design and its operation is knowledge-based, information-driven and largely automated. It will be competitive with fossil energies and other renewable energies, profitable for farmers and plant operators and favorable for the national economy. In this paper we discuss the required contribution of research to achieve these aims.
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Process Disturbances in Agricultural Biogas Production—Causes, Mechanisms and Effects on the Biogas Microbiome: A Review. ENERGIES 2019. [DOI: 10.3390/en12030365] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Disturbances of the anaerobic digestion process reduce the economic and environmental performance of biogas systems. A better understanding of the highly complex process is of crucial importance in order to avoid disturbances. This review defines process disturbances as significant changes in the functionality within the microbial community leading to unacceptable and severe decreases in biogas production and requiring an active counteraction to be overcome. The main types of process disturbances in agricultural biogas production are classified as unfavorable process temperatures, fluctuations in the availability of macro- and micronutrients (feedstock variability), overload of the microbial degradation potential, process-related accumulation of inhibiting metabolites such as hydrogen (H2), ammonium/ammonia (NH4+/NH3) or hydrogen sulphide (H2S) and inhibition by other organic and inorganic toxicants. Causes, mechanisms and effects on the biogas microbiome are discussed. The need for a knowledge-based microbiome management to ensure a stable and efficient production of biogas with low susceptibility to disturbances is derived and an outlook on potential future process monitoring and control by means of microbial indicators is provided.
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New concepts in anaerobic digestion processes: recent advances and biological aspects. Appl Microbiol Biotechnol 2018; 102:5065-5076. [DOI: 10.1007/s00253-018-9039-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
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Medicinal Application of Synthetic Biology. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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