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Abstract
Microbial communities are constantly challenged with environmental stressors, such as antimicrobials, pollutants, and global warming. How do they respond to these changes? Answering this question is crucial given that microbial communities perform essential functions for life on Earth. Our research aims to understand and predict communities' responses to change by addressing the following questions. (i) How do eco-evolutionary feedbacks influence microbial community dynamics? (ii) How do multiple interacting species in a microbial community alter evolutionary processes? (iii) To what extent do microbial communities respond to change by ecological versus evolutionary processes? To answer these questions, we use microbial communities of reduced complexity coupled with experimental evolution, genome sequencing, and mathematical modeling. The overall expectation from this integrative research approach is to generate general concepts that extend beyond specific bacterial species and provide fundamental insights into the consequences of evolution on the functioning of whole microbial communities.
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52
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Tal O, Bartuv R, Vetcos M, Medina S, Jiang J, Freilich S. NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. Microorganisms 2021; 9:microorganisms9091838. [PMID: 34576734 PMCID: PMC8468097 DOI: 10.3390/microorganisms9091838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/08/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
The study of microbial activity can be viewed as a triangle with three sides: environment (dominant resources in a specific habitat), community (species dictating a repertoire of metabolic conversions) and function (production and/or utilization of resources and compounds). Advances in metagenomics enable a high-resolution description of complex microbial communities in their natural environments and support a systematic study of environment-community-function associations. NetCom is a web-tool for predicting metabolic activities of microbial communities based on network-based interpretation of assembled and annotated metagenomics data. The algorithm takes as an input, lists of differentially abundant enzymatic reactions and generates the following outputs: (i) pathway associations of differently abundant enzymes; (ii) prediction of environmental resources that are unique to each treatment, and their pathway associations; (iii) prediction of compounds that are produced by the microbial community, and pathway association of compounds that are treatment-specific; (iv) network visualization of enzymes, environmental resources and produced compounds, that are treatment specific (2 and 3D). The tool is demonstrated on metagenomic data from rhizosphere and bulk soil samples. By predicting root-specific activities, we illustrate the relevance of our framework for forecasting the impact of soil amendments on the corresponding microbial communities. NetCom is available online.
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Affiliation(s)
- Ofir Tal
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Rotem Bartuv
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot 7628604, Israel
| | - Maria Vetcos
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Shlomit Medina
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China;
| | - Shiri Freilich
- Newe Ya’ar Research Center, Institute of Plant Sciences, The Agricultural Research Organization, Ramat Yishay 30095, Israel; (O.T.); (R.B.); (M.V.); (S.M.)
- Correspondence:
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53
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Abstract
Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.
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54
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Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals. ENERGIES 2021. [DOI: 10.3390/en14164903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.
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55
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Gralka M, Szabo R, Stocker R, Cordero OX. Trophic Interactions and the Drivers of Microbial Community Assembly. Curr Biol 2021; 30:R1176-R1188. [PMID: 33022263 DOI: 10.1016/j.cub.2020.08.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found in animal guts, oceans, or soils, it is still unclear whether there are generalizable biological or ecological processes that control their dynamics and function. Here, we review experimental and theoretical advances to argue that networks of trophic interactions, in which the metabolic excretions of one species are the primary resource for another, constitute the central drivers of microbial community assembly. Trophic interactions emerge from the deconstruction of complex forms of organic matter into a wealth of smaller metabolic intermediates, some of which are released to the environment and serve as a nutritional buffet for the community. The structure of the emergent trophic network and the rate at which primary resources are supplied control many features of microbial community assembly, including the relative contributions of competition and cooperation and the emergence of alternative community states. Viewing microbial community assembly through the lens of trophic interactions also has important implications for the spatial dynamics of communities as well as the functional redundancy of taxonomic groups. Given the ubiquity of trophic interactions across environments, they impart a common logic that can enable the development of a more quantitative and predictive microbial community ecology.
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Affiliation(s)
- Matti Gralka
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rachel Szabo
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich 8093, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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56
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Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel. NPJ Biofilms Microbiomes 2021; 7:64. [PMID: 34354076 PMCID: PMC8342524 DOI: 10.1038/s41522-021-00233-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
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57
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Ibrahim M, Raajaraam L, Raman K. Modelling microbial communities: Harnessing consortia for biotechnological applications. Comput Struct Biotechnol J 2021; 19:3892-3907. [PMID: 34584635 PMCID: PMC8441623 DOI: 10.1016/j.csbj.2021.06.048] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Microbes propagate and thrive in complex communities, and there are many benefits to studying and engineering microbial communities instead of single strains. Microbial communities are being increasingly leveraged in biotechnological applications, as they present significant advantages such as the division of labour and improved substrate utilisation. Nevertheless, they also present some interesting challenges to surmount for the design of efficient biotechnological processes. In this review, we discuss key principles of microbial interactions, followed by a deep dive into genome-scale metabolic models, focussing on a vast repertoire of constraint-based modelling methods that enable us to characterise and understand the metabolic capabilities of microbial communities. Complementary approaches to model microbial communities, such as those based on graph theory, are also briefly discussed. Taken together, these methods provide rich insights into the interactions between microbes and how they influence microbial community productivity. We finally overview approaches that allow us to generate and test numerous synthetic community compositions, followed by tools and methodologies that can predict effective genetic interventions to further improve the productivity of communities. With impending advancements in high-throughput omics of microbial communities, the stage is set for the rapid expansion of microbial community engineering, with a significant impact on biotechnological processes.
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Affiliation(s)
- Maziya Ibrahim
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Lavanya Raajaraam
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
| | - Karthik Raman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai 600 036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai 600 036, India
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58
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Zhang H, Serwah Boateng NA, Ngolong Ngea GL, Shi Y, Lin H, Yang Q, Wang K, Zhang X, Zhao L, Droby S. Unravelling the fruit microbiome: The key for developing effective biological control strategies for postharvest diseases. Compr Rev Food Sci Food Saf 2021; 20:4906-4930. [PMID: 34190408 DOI: 10.1111/1541-4337.12783] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/15/2022]
Abstract
Fruit-based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from these microbial communities is considered relevant to the field of biological control in prevention of postharvest fruit pathology. In this study, the importance of the microbiome of certain fruits and how it holds promise for solving the problems inherent in biocontrol and postharvest crop protection are summarized. Research needs on the fruit microbiome are highlighted. Data from DNA sequencing and "meta-omics" technologies very recently applied to the study of microbial communities of fruits in the postharvest context are also discussed. Various fruit parameters, management practices, and environmental conditions are the main determinants of the microbiome. Microbial communities can be classified according to their structure and function in fruit tissues. A critical mechanism of microbial biological control agents is to reshape and interact with the microbiome of the fruit. The ability to control the microbiome of any fruit is a great potential in postharvest management of fruits. Research on the fruit microbiome offers important opportunities to develop postharvest biocontrol strategies and products, as well as the health profile of the fruit.
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Affiliation(s)
- Hongyin Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | | | - Guillaume Legrand Ngolong Ngea
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China.,Institute of Fisheries Sciences, University of Douala, Douala, Cameroon
| | - Yu Shi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Hetong Lin
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiya Yang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Kaili Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Xiaoyun Zhang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Lina Zhao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Rishon LeZion, Israel
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59
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Nogueira T, Botelho A. Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. Antibiotics (Basel) 2021; 10:787. [PMID: 34203511 PMCID: PMC8300701 DOI: 10.3390/antibiotics10070787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
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Affiliation(s)
- Teresa Nogueira
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Evolutionary Ecology of Microorganisms Group, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Botelho
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
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60
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Yamagishi JF, Saito N, Kaneko K. Adaptation of metabolite leakiness leads to symbiotic chemical exchange and to a resilient microbial ecosystem. PLoS Comput Biol 2021; 17:e1009143. [PMID: 34161322 PMCID: PMC8260005 DOI: 10.1371/journal.pcbi.1009143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/06/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023] Open
Abstract
Microbial communities display remarkable diversity, facilitated by the secretion of chemicals that can create new niches. However, it is unclear why cells often secrete even essential metabolites after evolution. Based on theoretical results indicating that cells can enhance their own growth rate by leaking even essential metabolites, we show that such "leaker" cells can establish an asymmetric form of mutualism with "consumer" cells that consume the leaked chemicals: the consumer cells benefit from the uptake of the secreted metabolites, while the leaker cells also benefit from such consumption, as it reduces the metabolite accumulation in the environment and thereby enables further secretion, resulting in frequency-dependent coexistence of multiple microbial species. As supported by extensive simulations, such symbiotic relationships generally evolve when each species has a complex reaction network and adapts its leakiness to optimize its own growth rate under crowded conditions and nutrient limitations. Accordingly, symbiotic ecosystems with diverse cell species that leak and exchange many metabolites with each other are shaped by cell-level adaptation of leakiness of metabolites. Moreover, the resultant ecosystems with entangled metabolite exchange are resilient against structural and environmental perturbations. Thus, we present a theory for the origin of resilient ecosystems with diverse microbes mediated by secretion and exchange of essential chemicals.
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Affiliation(s)
- Jumpei F. Yamagishi
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Nen Saito
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Kunihiko Kaneko
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro-ku, Tokyo, Japan
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61
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Kapoore RV, Padmaperuma G, Maneein S, Vaidyanathan S. Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing. Crit Rev Biotechnol 2021; 42:46-72. [PMID: 33980092 DOI: 10.1080/07388551.2021.1921691] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.
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Affiliation(s)
- Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Gloria Padmaperuma
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Supattra Maneein
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Pharmaceutical, Chemical & Environmental Sciences, The University of Greenwich, Kent, UK
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62
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Dubey M, Hadadi N, Pelet S, Carraro N, Johnson DR, van der Meer JR. Environmental connectivity controls diversity in soil microbial communities. Commun Biol 2021; 4:492. [PMID: 33888858 PMCID: PMC8062517 DOI: 10.1038/s42003-021-02023-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/24/2021] [Indexed: 01/03/2023] Open
Abstract
Interspecific interactions are thought to govern the stability and functioning of microbial communities, but the influence of the spatial environment and its structural connectivity on the potential of such interactions to unfold remain largely unknown. Here we studied the effects on community growth and microbial diversity as a function of environmental connectivity, where we define environmental connectivity as the degree of habitat fragmentation preventing microbial cells from living together. We quantitatively compared growth of a naturally-derived high microbial diversity community from soil in a completely mixed liquid suspension (high connectivity) to growth in a massively fragmented and poorly connected environment (low connectivity). The low connectivity environment consisted of homogenously-sized miniature agarose beads containing random single or paired founder cells. We found that overall community growth was the same in both environments, but the low connectivity environment dramatically reduced global community-level diversity compared to the high connectivity environment. Experimental observations were supported by community growth modeling. The model predicts a loss of diversity in the low connectivity environment as a result of negative interspecific interactions becoming more dominant at small founder species numbers. Counterintuitively for the low connectivity environment, growth of isolated single genotypes was less productive than that of random founder genotype cell pairs, suggesting that the community as a whole profited from emerging positive interspecific interactions. Our work demonstrates the importance of environmental connectivity for growth of natural soil microbial communities, which aids future efforts to intervene in or restore community composition to achieve engineering and biotechnological objectives. Manupriyam Dubey et al. use experimental systems with naturally derived soil microbiomes in liquid suspensions and encapsulated beads to compare community dynamics in well-connected and poorly connected environments. While their results show that microbial growth does not vary between conditions, they report that low connectivity led to reduced microbial diversity and suggest that these reductions in microbial diversity may be due to increased negative interspecific interactions.
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Affiliation(s)
- Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Noushin Hadadi
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Eawag, Dübendorf, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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63
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Qi M, Liang B, Zhang L, Ma X, Yan L, Dong W, Kong D, Zhang L, Zhu H, Gao SH, Jiang J, Liu SJ, Corvini PFX, Wang A. Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3270-3282. [PMID: 33566597 DOI: 10.1021/acs.est.0c06687] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.
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Affiliation(s)
- Mengyuan Qi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bin Liang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Long Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodan Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Lei Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenchen Dong
- Department of Civil and Natural Resources Engineering, University of Canterbury, Christchurch 8140, New Zealand
| | - Deyong Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liying Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Haizhen Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Hong Gao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Macchi M, Festa S, Nieto E, Irazoqui JM, Vega-Vela NE, Junca H, Valacco MP, Amadio AF, Morelli IS, Coppotelli BM. Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00588. [PMID: 33489789 PMCID: PMC7809168 DOI: 10.1016/j.btre.2021.e00588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023]
Abstract
Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.
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Affiliation(s)
- Marianela Macchi
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - Esteban Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
| | - José M. Irazoqui
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Nelson E. Vega-Vela
- Pontificia Universidad Javeriana, Bogotá, Colombia
- Universidad de Bogotá Jorge Tadeo Lozano, Bogotá, Colombia
| | - Howard Junca
- Microbiomas Foundation, Div. Ecogenomics & Holobionts, RG Microbial Ecology: Metabolism, Genomics & Evolution, Chía, Colombia
| | | | - Ariel F. Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Irma S. Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M. Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CINDEFI (UNLP, CCT-La Plata, CONICET), La Plata, Argentina
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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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66
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Esposito A. Cooperation of partially-transformed clones: an invisible force behind the early stages of carcinogenesis. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201532. [PMID: 33594337 PMCID: PMC7116746 DOI: 10.1098/rsos.201532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
1Most tumours exhibit significant heterogeneity and are best described as communities of cellular populations competing for resources. Growing experimental evidence also suggests, however, that cooperation between cancer clones is important as well for the maintenance of tumour heterogeneity and tumour progression. However, a role for cell communication during the earliest steps in oncogenesis is not well characterised despite its vital importance in normal tissue and clinically manifest tumours. Here, we present a simple analytical model and stochastic lattice-based simulations to study how the interaction between the mutational process and cell-to-cell communication in three-dimensional tissue architecture might contribute to shape early oncogenesis. We show that non-cell-autonomous mechanisms of carcinogenesis could support and accelerate pre-cancerous clonal expansion through the cooperation of different, non- or partially- transformed mutants. We predict the existence of a 'cell-autonomous time-horizon', a time before which cooperation between cell-to-cell communication and DNA mutations might be one of the most fundamental forces shaping the early stages of oncogenesis. The understanding of this process could shed new light on the mechanisms leading to clinically manifest cancers.
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Affiliation(s)
- Alessandro Esposito
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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67
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Kurkjian HM, Akbari MJ, Momeni B. The impact of interactions on invasion and colonization resistance in microbial communities. PLoS Comput Biol 2021; 17:e1008643. [PMID: 33481772 PMCID: PMC7857599 DOI: 10.1371/journal.pcbi.1008643] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 02/03/2021] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions of resident members with the invader. Here we study how interactions influence invasion outcomes in microbial communities, when interactions are primarily mediated by chemicals that are released into or consumed from the environment. We use a previously developed dynamic model which explicitly includes species abundances and the concentrations of chemicals that mediate species interaction. Using this model, we assessed how species interactions impact invasion by simulating a new species being introduced into an existing resident community. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or decreased and whether the invader was maintained in the community or went extinct. We found that as the number of invaders introduced into the resident community increased, disruption rather than augmentation became more prevalent. With more facilitation of the invader by the resident community, resistance outcomes were replaced by displacement and augmentation. By contrast, with more facilitation among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, the majority of augmentation outcomes turned into displacement, while when inhibition of residents by invaders was eliminated, invasion outcomes were largely unaffected. Our results suggest that a better understanding of interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities. Our resident microbiota can prevent diseases by making it harder for pathogens to grow and establish, a phenomenon called “colonization resistance.” Colonization resistance is one of the major benefits provided by human-associated microbiota and a viable alternative to the use of antibiotics for preventing or treating infections. Here we use a model of microbial interactions through production and consumption of metabolic compounds to assay invasion and colonization resistance. We systematically examine in simulations how interactions among resident members and those between residents and an invader impact colonization resistance and invasion outcomes. In our simulations, the common strategy of increasing the dosage of probiotics is often unsuccessful for augmenting a new species into a resident microbiota. Instead, we find that the net facilitation or inhibition between the resident members and the invader explains whether the community remains intact and whether the invader can establish. Our results suggest that a better understanding of microbial interactions can inform successful microbiota interventions.
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Affiliation(s)
- Helen M. Kurkjian
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - M. Javad Akbari
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Babak Momeni
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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Li E, Deng T, Yan L, Zhou J, He Z, Deng Y, Xu M. Elevated nitrate simplifies microbial community compositions and interactions in sulfide-rich river sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141513. [PMID: 32853935 DOI: 10.1016/j.scitotenv.2020.141513] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Excessive nitrate in water systems is prevailing and a global risk of human health. Polluted river sediments are dominated by anaerobes and often the hotspot of denitrification. So far, little is known about the ecological effects of nitrate pollution on microbial dynamics, especially those in sulfide-rich sediments. Here we simulated a nitrate surge and monitored the microbial responses, as well as the changes of important environmental parameters in a sulfide-rich river sediment for a month. Our analysis of sediment microbial communities showed that elevated nitrate led to (i) a functional convergence at denitrification and sulfide oxidation, (ii) a taxonomic convergence at Proteobacteria, and (iii) a significant loss of biodiversity, community stability and other functions. Two chemolithotrophic denitrifiers Thiobacillus and Luteimonas were enriched after nitrate amendment, although the original communities were dominated by methanogens and syntrophic bacteria. Also, serial dilutions of sediment microbial communities found that Thiobacillus thiophilus dominated 18/30 communities because of its capability of simultaneous nitrate reduction and sulfide oxidation. Additionally, our network analysis indicated that keystone taxa seemed more likely to be native auxotrophs (e.g., syntrophic bacteria, methanogens) rather than dominant denitrifiers, possibly because of the extensive interspecific cross-feeding they estabilished, while environment perturbations probably disrupted that cross-feeding and simplified microbial interactions. This study advances our understanding of microbial community responses to nitrate pollution and possible mechanism in the sulfide-rich river sediment.
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Affiliation(s)
- Enze Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
| | - Tongchu Deng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
| | - Lei Yan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, China.
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69
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Marek A, Opalek M, Kałdon A, Mickowska B, Wloch-Salamon D. Hypersensitive SSY1 mutations negatively influence transition to quiescence in yeast Saccharomyces cerevisiae. Yeast 2020; 38:102-116. [PMID: 33179371 DOI: 10.1002/yea.3536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/28/2020] [Accepted: 11/02/2020] [Indexed: 01/20/2023] Open
Abstract
Most cells spend the majority of their life in the non-proliferating, quiescent state. Transition to this state is crucial for microorganisms to survive long starvation periods and restart divisions afterwards. Experimental evolution allowed us to identify several mutation in genes that are presumably important for such transition in yeast cells. Most of these candidate genes belong to the SPS amino acid sensing pathway or to the SIR complex. We assembled these mutations on the ancestral strain background. Analysis of the quiescent/non-quiescent cell ratio of the starved yeast populations confirmed the crucial role of SSY1, the primary receptor component of the SPS sensor, in transition to the Q state. The evolved SSY1 mutations increased yeast sensitivity to amino acid presence in the environment. This resulted in decreased quiescent cell fraction and a 5.14% increase of the total amino acid content in the starved populations. We discuss external amino acid sensing via the SPS pathway as one of the mechanisms influencing transition to quiescence.
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Affiliation(s)
- Agnieszka Marek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Aleksandra Kałdon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
| | - Barbara Mickowska
- Faculty of Food Technology, Malopolska Centre of Food Monitoring, University of Agriculture in Krakow, Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, Poland
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70
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Frank BP, Goodwin DG, Bohutskyi P, Phan DC, Lu X, Kuwama L, Bouwer EJ, Fairbrother DH. Influence of polymer type and carbon nanotube properties on carbon nanotube/polymer nanocomposite biodegradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140512. [PMID: 32721719 DOI: 10.1016/j.scitotenv.2020.140512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The interaction of anaerobic microorganisms with carbon nanotube/polymer nanocomposites (CNT/PNC) will play a major role in determining their persistence and environmental fate at the end of consumer use when these nano-enabled materials enter landfills and encounter wastewater. Motivated by the need to understand how different parameters (i.e., polymer type, microbial phenotype, CNT characteristics) influence CNT/PNC biodegradation rates, we have used volumetric biogas measurements and kinetic modeling to study biodegradation as a function of polymer type and CNT properties. In one set of experiments, oxidized multiwall carbon nanotubes (O-MWCNTs) with a range of CNT loadings 0-5% w/w were incorporated into poly-ε-caprolactone (PCL) and polyhydroxyalkanoates (PHA) matrices and subjected to biodegradation by an anaerobic microbial community. For each CNT/PNC, complete polymer biodegradation was ultimately observed, although the rate of biodegradation was inhibited above certain critical CNT loadings dependent upon the polymer type. Higher loadings of pristine MWCNTs were needed to decrease the rate of polymer biodegradation compared to O-MWCNTs, an effect ascribed principally to differences in CNT dispersion within the polymer matrices. Above certain CNT loadings, a CNT mat of similar shape to the initial PNC was formed after polymer biodegradation, while below this threshold, CNT aggregates fragmented in the media. In situations where biodegradation was rapid, methanogen growth was disproportionately inhibited compared to the overall microbial community. Analysis of the results obtained from this study indicates that the inhibitory effect of CNTs on polymer biodegradation rate is greatest under conditions (i.e., polymer type, microbial phenotype, CNT dispersion) where biodegradation of the neat polymer is slowest. This new insight provides a means to predict the environmental fate, persistence, and transformations of CNT-enabled polymer materials.
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Affiliation(s)
- Benjamin P Frank
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - David G Goodwin
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Pavlo Bohutskyi
- Biological Sciences Division, Pacific Northwest National Laboratory, 3300 Stevens Dr., Richland, Washington 99354, United States
| | - Duc C Phan
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States; Department of Civil and Environmental Engineering, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX 78249, United States
| | - Xier Lu
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Leo Kuwama
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - Edward J Bouwer
- Department of Environmental Health and Engineering, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States
| | - D Howard Fairbrother
- Department of Chemistry, Johns Hopkins University, 3400 N Charles St., Baltimore, MD 21218, United States.
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Cooper RE, Wegner CE, Kügler S, Poulin RX, Ueberschaar N, Wurlitzer JD, Stettin D, Wichard T, Pohnert G, Küsel K. Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms. THE ISME JOURNAL 2020; 14:2675-2690. [PMID: 32690937 PMCID: PMC7784907 DOI: 10.1038/s41396-020-0718-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/30/2020] [Accepted: 07/08/2020] [Indexed: 02/02/2023]
Abstract
Coexistence of microaerophilic Fe(II)-oxidizers and anaerobic Fe(III)-reducers in environments with fluctuating redox conditions is a prime example of mutualism, in which both partners benefit from the sustained Fe-pool. Consequently, the Fe-cycling machineries (i.e., metal-reducing or -oxidizing pathways) should be most affected during co-cultivation. However, contrasting growth requirements impeded systematic elucidation of their interactions. To disentangle underlying interaction mechanisms, we established a suboxic co-culture system of Sideroxydans sp. CL21 and Shewanella oneidensis. We showed that addition of the partner's cell-free supernatant enhanced both growth and Fe(II)-oxidizing or Fe(III)-reducing activity of each partner. Metabolites of the exometabolome of Sideroxydans sp. CL21 are generally upregulated if stimulated with the partner´s spent medium, while S. oneidensis exhibits a mixed metabolic response in accordance with a balanced response to the partner. Surprisingly, RNA-seq analysis revealed genes involved in Fe-cycling were not differentially expressed during co-cultivation. Instead, the most differentially upregulated genes included those encoding for biopolymer production, lipoprotein transport, putrescine biosynthesis, and amino acid degradation suggesting a regulated inter-species biofilm formation. Furthermore, the upregulation of hydrogenases in Sideroxydans sp. CL21 points to competition for H2 as electron donor. Our findings reveal that a complex metabolic and transcriptomic response, but not accelerated formation of Fe-end products, drive interactions of Fe-cycling microorganisms.
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Affiliation(s)
- Rebecca E Cooper
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Stefan Kügler
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Remington X Poulin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Nico Ueberschaar
- Mass Spectrometry Platform, Faculty of Chemistry and Earth Sciences, Friedrich Schiller University Jena, Humboldstr. 8, 07743, Jena, Germany
| | - Jens D Wurlitzer
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany
| | - Daniel Stettin
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Thomas Wichard
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, 07743, Jena, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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Regularized S-Map Reveals Varying Bacterial Interactions. Appl Environ Microbiol 2020; 86:AEM.01615-20. [PMID: 32801185 DOI: 10.1128/aem.01615-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
There is a growing awareness that bacterial interactions follow a highly nonlinear pattern in reality. However, it is challenging to track the varying bacterial interactions using pairwise correlation analysis, which fails to explore their potential effects on the behavior of microbes. Here, we utilized a regularized sequential locally weighted global linear map (S-map) to capture the varying interspecific interactions from the time series data of a bacterial community under exposure to nitrite. Our results show that bacterial interactions are highly variable and that asymmetric interactions dominate the interaction pattern in a community. Furthermore, we propose a Jacobian coefficient-based statistical method to predict the harmony level of a bacterial community at each successive ecosystem state. The results show that the bacterial community exhibits a higher harmony level in nitrite-treated samples than in the control group. We show that the community harmony level is positively associated with the specific endogenous respiration rates and biofilm formation of the culture. In addition, the community tends to process lower diversity and structural stability under zero- and high-nitrite stresses. We demonstrate that the harmony level, rather than structural stability, is a useful index for unveiling the underlying mechanism of bacterial performance. Overall, the regularized S-map can help us to understand bacterial interactions in ecosystems more accurately than previous approaches.IMPORTANCE It has long been acknowledged that bacterial interactions play important roles in community structure and function. Revealing the interaction variability can allow an understanding of how bacteria respond to perturbation and why bacterial community performance changes. Such information should improve our skills in engineering bacterial communities (e.g., in a wastewater treatment plant) and achieve better removal performance and lower energy consumption.
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Integrated Metabolic Modeling, Culturing, and Transcriptomics Explain Enhanced Virulence of Vibrio cholerae during Coinfection with Enterotoxigenic Escherichia coli. mSystems 2020; 5:5/5/e00491-20. [PMID: 32900868 PMCID: PMC7483508 DOI: 10.1128/msystems.00491-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections. Gene essentiality is altered during polymicrobial infections. Nevertheless, most studies rely on single-species infections to assess pathogen gene essentiality. Here, we use genome-scale metabolic models (GEMs) to explore the effect of coinfection of the diarrheagenic pathogen Vibrio cholerae with another enteric pathogen, enterotoxigenic Escherichia coli (ETEC). Model predictions showed that V. cholerae metabolic capabilities were increased due to ample cross-feeding opportunities enabled by ETEC. This is in line with increased severity of cholera symptoms known to occur in patients with dual infections by the two pathogens. In vitro coculture systems confirmed that V. cholerae growth is enhanced in cocultures relative to single cultures. Further, expression levels of several V. cholerae metabolic genes were significantly perturbed as shown by dual RNA sequencing (RNAseq) analysis of its cocultures with different ETEC strains. A decrease in ETEC growth was also observed, probably mediated by nonmetabolic factors. Single gene essentiality analysis predicted conditionally independent genes that are essential for the pathogen’s growth in both single-infection and coinfection scenarios. Our results reveal growth differences that are of relevance to drug targeting and efficiency in polymicrobial infections. IMPORTANCE Most studies proposing new strategies to manage and treat infections have been largely focused on identifying druggable targets that can inhibit a pathogen's growth when it is the single cause of infection. In vivo, however, infections can be caused by multiple species. This is important to take into account when attempting to develop or use current antibacterials since their efficacy can change significantly between single infections and coinfections. In this study, we used genome-scale metabolic models (GEMs) to interrogate the growth capabilities of Vibrio cholerae in single infections and coinfections with enterotoxigenic E. coli (ETEC), which cooccur in a large fraction of diarrheagenic patients. Coinfection model predictions showed that V. cholerae growth capabilities are enhanced in the presence of ETEC relative to V. cholerae single infection, through cross-fed metabolites made available to V. cholerae by ETEC. In vitro, cocultures of the two enteric pathogens further confirmed model predictions showing an increased growth of V. cholerae in coculture relative to V. cholerae single cultures while ETEC growth was suppressed. Dual RNAseq analysis of the cocultures also confirmed that the transcriptome of V. cholerae was distinct during coinfection compared to single-infection scenarios where processes related to metabolism were significantly perturbed. Further, in silico gene-knockout simulations uncovered discrepancies in gene essentiality for V. cholerae growth between single infections and coinfections. Integrative model-guided analysis thus identified druggable targets that would be critical for V. cholerae growth in both single infections and coinfections; thus, designing inhibitors against those targets would provide a broader spectrum of coverage against cholera infections.
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Henriques SF, Dhakan DB, Serra L, Francisco AP, Carvalho-Santos Z, Baltazar C, Elias AP, Anjos M, Zhang T, Maddocks ODK, Ribeiro C. Metabolic cross-feeding in imbalanced diets allows gut microbes to improve reproduction and alter host behaviour. Nat Commun 2020; 11:4236. [PMID: 32843654 PMCID: PMC7447780 DOI: 10.1038/s41467-020-18049-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
The impact of commensal bacteria on the host arises from complex microbial-diet-host interactions. Mapping metabolic interactions in gut microbial communities is therefore key to understand how the microbiome influences the host. Here we use an interdisciplinary approach including isotope-resolved metabolomics to show that in Drosophila melanogaster, Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) a syntrophic relationship is established to overcome detrimental host diets and identify Ap as the bacterium altering the host's feeding decisions. Specifically, we show that Ap uses the lactate produced by Lp to supply amino acids that are essential to Lp, allowing it to grow in imbalanced diets. Lactate is also necessary and sufficient for Ap to alter the fly's protein appetite. Our data show that gut bacterial communities use metabolic interactions to become resilient to detrimental host diets. These interactions also ensure the constant flow of metabolites used by the microbiome to alter reproduction and host behaviour.
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Affiliation(s)
- Sílvia F Henriques
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Darshan B Dhakan
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Lúcia Serra
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Patrícia Francisco
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Zita Carvalho-Santos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Célia Baltazar
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Ana Paula Elias
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Margarida Anjos
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Tong Zhang
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Oliver D K Maddocks
- University of Glasgow Institute of Cancer Sciences, Switchback Road, Glasgow, G61 1QH, UK
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal.
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75
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Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community. ISME JOURNAL 2020; 14:2816-2828. [PMID: 32788711 DOI: 10.1038/s41396-020-00737-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 01/12/2023]
Abstract
Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
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76
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Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. Nat Commun 2020; 11:3803. [PMID: 32732991 PMCID: PMC7393147 DOI: 10.1038/s41467-020-17612-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
Microbial communities comprised of phototrophs and heterotrophs hold great promise for sustainable biotechnology. Successful application of these communities relies on the selection of appropriate partners. Here we construct four community metabolic models to guide strain selection, pairing phototrophic, sucrose-secreting Synechococcus elongatus with heterotrophic Escherichia coli K-12, Escherichia coli W, Yarrowia lipolytica, or Bacillus subtilis. Model simulations reveae metabolic exchanges that sustain the heterotrophs in minimal media devoid of any organic carbon source, pointing to S. elongatus-E. coli K-12 as the most active community. Experimental validation of flux predictions for this pair confirms metabolic interactions and potential production capabilities. Synthetic communities bypass member-specific metabolic bottlenecks (e.g. histidine- and transport-related reactions) and compensate for lethal genetic traits, achieving up to 27% recovery from lethal knockouts. The study provides a robust modelling framework for the rational design of synthetic communities with optimized growth sustainability using phototrophic partners.
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77
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Opalek M, Wloch-Salamon D. Aspects of Multicellularity in Saccharomyces cerevisiae Yeast: A Review of Evolutionary and Physiological Mechanisms. Genes (Basel) 2020; 11:genes11060690. [PMID: 32599749 PMCID: PMC7349301 DOI: 10.3390/genes11060690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this promotes facultative multicellularity in S. cerevisiae. We first describe proximate mechanisms leading to aggregation. These mechanisms include staying together and coming together, and can lead to group heterogeneity. Heterogeneity is promoted by nutrient limitation, structured environments and aging. We then characterize the evolutionary benefits and costs of facultative multicellularity in yeast. We summarize current knowledge and focus on the newest state-of-the-art discoveries that will fuel future research programmes aiming to understand facultative microbial multicellularity.
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78
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Chen F, Wegner SV. Blue-Light-Switchable Bacterial Cell-Cell Adhesions Enable the Control of Multicellular Bacterial Communities. ACS Synth Biol 2020; 9:1169-1180. [PMID: 32243746 DOI: 10.1021/acssynbio.0c00054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the fundamental importance and biotechnological potential of multibacterial communities, also called biofilms, are well-known, our ability to control them is limited. We present a new way of dynamically controlling bacteria-bacteria adhesions by using blue light and how these photoswitchable adhesions can be used to regulate multicellularity and associated bacterial behavior. To achieve this, the photoswitchable proteins nMagHigh and pMagHigh were expressed on bacterial surfaces as adhesins to allow multicellular clusters to assemble under blue light and reversibly disassemble in the dark. Regulation of the bacterial cell-cell adhesions with visible light provides unique advantages including high spatiotemporal control, tunability, and noninvasive remote regulation. Moreover, these photoswitchable adhesions make it possible to regulate collective bacterial functions including aggregation, quorum sensing, biofilm formation, and metabolic cross-feeding between auxotrophic bacteria with light. Overall, the photoregulation of bacteria-bacteria adhesions provides a new way of studying bacterial cell biology and will enable the design of biofilms for biotechnological applications.
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Affiliation(s)
- Fei Chen
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
| | - Seraphine V. Wegner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, 48149 Münster, Germany
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79
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Flores AD, Choi HG, Martinez R, Onyeabor M, Ayla EZ, Godar A, Machas M, Nielsen DR, Wang X. Catabolic Division of Labor Enhances Production of D-Lactate and Succinate From Glucose-Xylose Mixtures in Engineered Escherichia coli Co-culture Systems. Front Bioeng Biotechnol 2020; 8:329. [PMID: 32432089 PMCID: PMC7214542 DOI: 10.3389/fbioe.2020.00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
Although biological upgrading of lignocellulosic sugars represents a promising and sustainable route to bioplastics, diverse and variable feedstock compositions (e.g., glucose from the cellulose fraction and xylose from the hemicellulose fraction) present several complex challenges. Specifically, sugar mixtures are often incompletely metabolized due to carbon catabolite repression while composition variability further complicates the optimization of co-utilization rates. Benefiting from several unique features including division of labor, increased metabolic diversity, and modularity, synthetic microbial communities represent a promising platform with the potential to address persistent bioconversion challenges. In this work, two unique and catabolically orthogonal Escherichia coli co-cultures systems were developed and used to enhance the production of D-lactate and succinate (two bioplastic monomers) from glucose-xylose mixtures (100 g L-1 total sugars, 2:1 by mass). In both cases, glucose specialist strains were engineered by deleting xylR (encoding the xylose-specific transcriptional activator, XylR) to disable xylose catabolism, whereas xylose specialist strains were engineered by deleting several key components involved with glucose transport and phosphorylation systems (i.e., ptsI, ptsG, galP, glk) while also increasing xylose utilization by introducing specific xylR mutations. Optimization of initial population ratios between complementary sugar specialists proved a key design variable for each pair of strains. In both cases, ∼91% utilization of total sugars was achieved in mineral salt media by simple batch fermentation. High product titer (88 g L-1 D-lactate, 84 g L-1 succinate) and maximum productivity (2.5 g L-1 h-1 D-lactate, 1.3 g L-1 h-1 succinate) and product yield (0.97 g g-total sugar-1 for D-lactate, 0.95 g g-total sugar-1 for succinate) were also achieved.
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Affiliation(s)
- Andrew D. Flores
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Hyun G. Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - E. Zeynep Ayla
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Amanda Godar
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Michael Machas
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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80
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Schlundt C, Mark Welch JL, Knochel AM, Zettler ER, Amaral‐Zettler LA. Spatial structure in the "Plastisphere": Molecular resources for imaging microscopic communities on plastic marine debris. Mol Ecol Resour 2020; 20:620-634. [PMID: 31782619 PMCID: PMC7318237 DOI: 10.1111/1755-0998.13119] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/21/2019] [Accepted: 11/05/2019] [Indexed: 12/01/2022]
Abstract
Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and microbes in the "Plastisphere"-the thin layer of life on the surface of PMD-has been technology-limited. Research into microbe-microbe and microbe-substrate interactions requires knowledge of community phylogenetic composition but also tools to visualize spatial distributions of intact microbial biofilm communities. We developed a CLASI-FISH (combinatorial labelling and spectral imaging - fluorescence in situ hybridization) method using confocal microscopy to study Plastisphere communities. We created a probe set consisting of three existing phylogenetic probes (targeting all Bacteria, Alpha-, and Gammaproteobacteria) and four newly designed probes (targeting Bacteroidetes, Vibrionaceae, Rhodobacteraceae and Alteromonadaceae) labelled with a total of seven fluorophores and validated this probe set using pure cultures. Our nested probe set strategy increases confidence in taxonomic identification because targets are confirmed with two or more probes, reducing false positives. We simultaneously identified and visualized these taxa and their spatial distribution within the microbial biofilms on polyethylene samples in colonization time series experiments in coastal environments from three different biogeographical regions. Comparing the relative abundance of 16S rRNA gene amplicon sequencing data with cell-count abundance data retrieved from the microscope images of the same samples showed a good agreement in bacterial composition. Microbial communities were heterogeneous, with direct spatial relationships between bacteria, cyanobacteria and eukaryotes such as diatoms but also micro-metazoa. Our research provides a valuable resource to investigate biofilm development, succession and associations between specific microscopic taxa at micrometre scales.
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Affiliation(s)
- Cathleen Schlundt
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMAUSA
| | - Jessica L. Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMAUSA
| | - Anna M. Knochel
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMAUSA
| | - Erik R. Zettler
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, TexelThe Netherlands
| | - Linda A. Amaral‐Zettler
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMAUSA
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen Burg, TexelThe Netherlands
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
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81
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Yang K, Xu M, Zhu J. Evaluating the Impact of Four Major Nutrients on Gut Microbial Metabolism by a Targeted Metabolomics Approach. J Proteome Res 2020; 19:1991-1998. [PMID: 32275156 DOI: 10.1021/acs.jproteome.9b00806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gut microbiome plays fundamental roles in host physiology, and gut microbial metabolism is important to the host-microbiome homeostasis. As major contributors to gut microbial metabolism, the medium nutritional components are essential to in vitro gut microbiome growths, and four nutrients, namely, inorganic salts, bile salts, short-chain fatty acids (SCFAs), and mucin, have gained particular attention because of their significant variation found in different growth environments and their ability to modulate the gut microbial population and functions. However, a systematic study is lacking to evaluate the effects of these four nutrients on the gut microbiome in terms of their impact on the microbial metabolic profiles. To fill the gap of the knowledge, we applied mass-spectrometry-based targeted metabolomics approach to study the regulation effects of these four medium components on in vitro-cultured gut microbiota. Our results show that inorganic salts and mucin had the greatest impacts on the gut microbiome metabolic profile compared to the other components studied, with gut microbial cultures grown with low-concentration inorganic salts and mucin-supplemented medium demonstrating greater numbers of metabolites detected. We also applied metabolic pathway impact analysis, which revealed several significantly impacted metabolic pathways during the comparison of different medium supplements, which could further assist our understanding of the overall impacts of certain critical nutrients on gut microbial metabolism. In summary, this pilot study can serve as a first attempt to evaluate the individual nutritional component in their contribution to gut microbial metabolic functions.
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Affiliation(s)
- Kundi Yang
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Mengyang Xu
- Cell, Molecular & Structural Biology Program, Miami University, Oxford, Ohio 45056, United States
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, Columbus, Ohio 43210, United States.,James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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82
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Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator. J Chem Ecol 2020; 46:659-667. [PMID: 32246258 DOI: 10.1007/s10886-020-01169-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/27/2020] [Accepted: 03/06/2020] [Indexed: 12/25/2022]
Abstract
Microbial metabolism can shape cues important for animal attraction in service-resource mutualisms. Resources are frequently colonized by microbial communities, but experimental assessment of animal-microbial interactions often focus on microbial monocultures. Such an approach likely fails to predict effects of microbial assemblages, as microbe-microbe interactions may affect in a non-additive manner microbial metabolism and resulting chemosensory cues. Here, we compared effects of microbial mono- and cocultures on growth of constituent microbes, volatile metabolite production, sugar catabolism, and effects on pollinator foraging across two nectar environments that differed in sugar concentration. Growth in co-culture decreased the abundance of the yeast Metschnikowia reukaufii, but not the bacterium Asaia astilbes. Volatile emissions differed significantly between microbial treatments and with nectar concentration, while sugar concentration was relatively similar among mono- and cocultures. Coculture volatile emission closely resembled an additive combination of monoculture volatiles. Despite differences in microbial growth and chemosensory cues, honey bee feeding did not differ between microbial monocultures and assemblages. Taken together, our results suggest that in some cases, chemical and ecological effects of microbial assemblages are largely predictable from those of component species, but caution that more work is necessary to predict under what circumstances non-additive effects are important.
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83
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Giri S, Shitut S, Kost C. Harnessing ecological and evolutionary principles to guide the design of microbial production consortia. Curr Opin Biotechnol 2020; 62:228-238. [DOI: 10.1016/j.copbio.2019.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023]
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84
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Ravikrishnan A, Blank LM, Srivastava S, Raman K. Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments. Comput Struct Biotechnol J 2020; 18:1249-1258. [PMID: 32551031 PMCID: PMC7286961 DOI: 10.1016/j.csbj.2020.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/10/2020] [Accepted: 03/20/2020] [Indexed: 01/13/2023] Open
Abstract
Microbial co-cultures have been used in several biotechnological applications. Within these co-cultures, the microorganisms tend to interact with each other and perform complex actions. Investigating metabolic interactions in microbial co-cultures is crucial in designing microbial consortia. Here, we present a pipeline integrating modelling and experimental approaches to understand metabolic interactions between organisms in a community. We define a new index named "Metabolic Support Index (MSI)", which quantifies the benefits derived by each organism in the presence of the other when grown as a co-culture. We computed MSI for several experimentally demonstrated co-cultures and showed that MSI, as a metric, accurately identifies the organism that derives the maximum benefit. We also computed MSI for a commonly used yeast co-culture consisting of Saccharomyces cerevisiae and Pichia stipitis and observed that the latter derives higher benefit from the interaction. Further, we designed two-stage experiments to study mutual interactions and showed that P. stipitis indeed derives the maximum benefit from the interaction, as shown from our computational predictions. Also, using our previously developed computational tool MetQuest, we identified all the metabolic exchanges happening between these organisms by analysing the pathways spanning the two organisms. By analysing the HPLC profiles and studying the isotope labelling, we show that P. stipitis consumes the ethanol produced by S. cerevisiae when grown on glucose-rich medium under aerobic conditions, as also indicated by our in silico pathway analyses. Our approach represents an important step in understanding metabolic interactions in microbial communities through an integrated computational and experimental workflow.
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Affiliation(s)
- Aarthi Ravikrishnan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Initiative for Biological Systems Engineering, IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, India
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology – ABBt, Worringer Weg 1, RWTH Aachen University, D-52074 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology – ABBt, Worringer Weg 1, RWTH Aachen University, D-52074 Aachen, Germany
| | - Smita Srivastava
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600 036, India
- Initiative for Biological Systems Engineering, IIT Madras, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, India
- Corresponding author.
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85
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Ezra-Nevo G, Henriques SF, Ribeiro C. The diet-microbiome tango: how nutrients lead the gut brain axis. Curr Opin Neurobiol 2020; 62:122-132. [PMID: 32199342 DOI: 10.1016/j.conb.2020.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/08/2020] [Indexed: 12/22/2022]
Abstract
Nutrients and the microbiome have a profound impact on the brain by influencing its development and function in health and disease. The mechanisms by which they shape brain function have only started to be uncovered. Here we propose that the interaction of diet with the microbiome is at the core of most mechanisms by which gut microbes affect host brain function. The microbiome acts on the host by altering the nutrients in the diet and by using them as precursors for synthetizing psychoactive metabolites. Diet is also a major modulator of gut microbiome composition making this another key mechanism by which they affect the host brain. Nutrient-microbiome-host interactions therefore provide an overarching framework to understand the function of the gut-brain axis.
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Affiliation(s)
- Gili Ezra-Nevo
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Sílvia F Henriques
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal
| | - Carlos Ribeiro
- Behavior and Metabolism Laboratory, Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, 1400-038, Portugal.
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86
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Lin TY, Wen RC, Shen CR, Tsai SL. Biotransformation of 5-Hydroxymethylfurfural to 2,5-Furandicarboxylic Acid by a Syntrophic Consortium of Engineered Synechococcus elongatus and Pseudomonas putida. Biotechnol J 2020; 15:e1900357. [PMID: 32181597 DOI: 10.1002/biot.201900357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/03/2020] [Indexed: 12/11/2022]
Abstract
2,5-furandicarboxylic acid (FDCA) is one of the top platform chemicals that can be produced from biomass feedstock. To make the cost of industrial FDCA production compatible with plastics made from fossils, the price of substrates and process complexity should be reduced. The aim of this research is to create a CO2 -driven syntrophic consortium for the catalytic conversion of renewable biomass-derived 5-hydroxymethylfurfural (HMF) to FDCA. Sucrose produced from carbon fixation by the engineered Synechococcus elongatus serves as the sole carbon source for the engineered Pseudomonas putida to catalyze the reaction of HMF to FDCA. The yield of FDCA by the consortium reaches around 70% while the conversion of HMF is close to 100%. With further surface engineering to clump the two strains, the FDCA yield is elevated to almost 100% via the specific association between an Src homology 3 (SH3) domain and its ligand. The syntrophic consortium successfully demonstrates its green and cost-effective characteristics for the conversion of CO2 and biomass into platform chemicals.
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Affiliation(s)
- Tzu-Yu Lin
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 10607, Taiwan
| | - Rex C Wen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Claire R Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, 10607, Taiwan
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87
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Arora D, Gupta P, Jaglan S, Roullier C, Grovel O, Bertrand S. Expanding the chemical diversity through microorganisms co-culture: Current status and outlook. Biotechnol Adv 2020; 40:107521. [PMID: 31953204 DOI: 10.1016/j.biotechadv.2020.107521] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/29/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Natural products (NPs) are considered as a cornerstone for the generation of bioactive leads in drug discovery programs. However, one of the major limitations of NP drug discovery program is "rediscovery" of known compounds, thereby hindering the rate of drug discovery efficiency. Therefore, in recent years, to overcome these limitations, a great deal of attention has been drawn towards understanding the role of microorganisms' co-culture in inducing novel chemical entities. Such induction could be related to activation of genes which might be silent or expressed at very low levels (below detection limit) in pure-strain cultures under normal laboratory conditions. In this review, chemical diversity of compounds isolated from microbial co-cultures, is discussed. For this purpose, chemodiversity has been represented as a chemical-structure network based on the "Tanimoto Structural Similarity Index". This highlights the huge structural diversity induced by microbial co-culture. In addition, the current trends in microbial co-culture research are highlighted. Finally, the current challenges (1 - induction monitoring, 2 - reproducibility, 3 - growth time effect and 4 - up-scaling for isolation purposes) are discussed. The information in this review will support researchers to design microbial co-culture strategies for future research efforts. In addition, guidelines for co-culture induction reporting are also provided to strengthen future reporting in this NP field.
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Affiliation(s)
- Divya Arora
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Prasoon Gupta
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Sundeep Jaglan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Catherine Roullier
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Olivier Grovel
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France.
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88
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Neira-Monsalve E, Wilches-Ramírez NC, Terán W, del Pilar Márquez M, Mosquera-Espinosa AT, Sáenz-Aponte A. Isolation, identification, and pathogenicity of Steinernema carpocapsae and its bacterial symbiont in Cauca-Colombia. J Nematol 2020; 52:e2020-89. [PMID: 33829195 PMCID: PMC8015356 DOI: 10.21307/jofnem-2020-089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Indexed: 11/30/2022] Open
Abstract
In Colombia, identification of entomopathogenic nematodes (EPN’s) native species is of great importance for pest management programs. The aim of this study was to isolate and identify EPNs and their bacterial symbiont in the department of Cauca-Colombia and then evaluate the susceptibility of two Hass avocado (Persea americana) pests to the EPNs isolated. EPNs were isolated from soil samples by the insect baiting technique. Their bacterial symbiont was isolated from hemolymph of infected Galleria mellonella larvae. Both organisms were molecularly identified. Morphological, and biochemical characterization was done for the bacteria. Susceptibility of Epitrix cucumeris and Pandeleteius cinereus adults was evaluated by individually exposing adults to 50 infective juveniles. EPNs were allegedly detected at two sampled sites (natural forest and coffee cultivation) in 5.8% of the samples analyzed. However, only natural forest EPN’s could be isolated and multiplied. The isolate was identified as Steinernema carpocapsae BPS and its bacterial symbiont as Xenorhabus nematophila BPS. Adults of both pests were susceptible to S. carpocapsae indicating this EPN potential for its management. The results of this study constitute the first record of S. carpocapsae in Colombia and the susceptibility of P. cinereus to this EPN.
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Affiliation(s)
- Esteban Neira-Monsalve
- Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana , Bogotá , Colombia
| | | | - Wilson Terán
- Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - María del Pilar Márquez
- Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana , Bogotá , Colombia
| | | | - Adriana Sáenz-Aponte
- Biología de Plantas y Sistemas Productivos, Departamento de Biología, Pontificia Universidad Javeriana , Bogotá , Colombia
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89
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Wang T, Goyal A, Dubinkina V, Maslov S. Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comput Biol 2019; 15:e1007524. [PMID: 31856158 PMCID: PMC6922320 DOI: 10.1371/journal.pcbi.1007524] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/01/2019] [Indexed: 11/30/2022] Open
Abstract
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of metabolic interactions between microbes, our model suggests about four trophic levels, each characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical metabolic environment of the gut (fecal metabolome) in approximate agreement with the real data. To understand the consequences of this trophic organization, we quantify the metabolic flow and biomass distribution, and explore patterns of microbial and metabolic diversity in different levels. The hierarchical trophic organization suggested by our model can help mechanistically establish causal links between the abundances of microbes and metabolites in the human gut.
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Affiliation(s)
- Tong Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Akshit Goyal
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Veronika Dubinkina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
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90
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Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
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Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
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91
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Feng Y, Zhao Y, Jiang B, Zhao H, Wang Q, Liu S. Discrepant gene functional potential and cross-feedings of anammox bacteria Ca. Jettenia caeni and Ca. Brocadia sinica in response to acetate. WATER RESEARCH 2019; 165:114974. [PMID: 31450220 DOI: 10.1016/j.watres.2019.114974] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Although the enhancement of anammox performance for wastewater treatment due to the addition of small amount of acetate has been reported, discrepant metabolic responses of different anammox species have not been experimentally evaluated. Based on metagenomics and metatranscriptomic data, we investigated the competitiveness between two typical anammox species, Candidatus Jettenia caeni (J. caeni) and Candidatus Brocadia sinica (B. sinica), in anammox consortia under mixotrophic condition, where complex metabolic interactions among anammox bacteria and heterotrophs also changed with acetate addition. Contrary to J. caeni, the dissimilatory nitrate reduction to ammonium pathway of B. sinica was markedly stimulated for improving nitrogen removal. More acetate metabolic pathways and up-regulated AMP-acs expression for acetyl-CoA synthesis in B. sinica contributed to its superiority in acetate utilization. Interestingly, cross-feedings, including the nitrogen cycle, amino acid cross-feeding and B-vitamin metabolic exchange between B. sinica and other heterotrophs seemed to be enhanced with acetate addition, contributing to a reduction in metabolic energy cost to the whole community. Our work not only clarified the mechanism underlying discrepant responses of different anammox species to acetate, but also suggests a possible strategy for obtaining higher nitrogen removal rates in wastewater treatment under low C/N ratio.
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Affiliation(s)
- Ying Feng
- Department of Environmental Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, 100871, China
| | - Yunpeng Zhao
- Department of Environmental Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, 100871, China
| | - Bo Jiang
- Department of Environmental Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, 100871, China
| | - Huazhang Zhao
- Department of Environmental Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, 100871, China
| | - Qilin Wang
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Sitong Liu
- Department of Environmental Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Water and Sediment Sciences, Ministry of Education of China, Beijing, 100871, China.
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92
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Inhibitory interaction networks among coevolved Streptomyces populations from prairie soils. PLoS One 2019; 14:e0223779. [PMID: 31671139 PMCID: PMC6822729 DOI: 10.1371/journal.pone.0223779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/29/2019] [Indexed: 12/24/2022] Open
Abstract
Soil microbes live within highly complex communities, where community composition, function, and evolution are the product of diverse interactions among community members. Analysis of the complex networks of interactions within communities has the potential to shed light on community stability, functioning, and evolution. However, we have little understanding of the variation in interaction networks among coevolved soil populations. We evaluated networks of antibiotic inhibitory interactions among sympatric Streptomyces communities from prairie soil. Inhibition networks differed significantly in key network characteristics from expectations under null models, largely reflecting variation among Streptomyces in the number of sympatric populations that they inhibited. Moreover, networks of inhibitory interactions within Streptomyces communities differed significantly from each other, suggesting unique network structures among soil communities from different locations. Analyses of tri-partite interactions (triads) showed that some triads were significantly over- or under- represented, and that communities differed in ‘preferred’ triads. These results suggest that local processes generate distinct structures among sympatric Streptomyces inhibition networks in soil. Understanding the properties of microbial interaction networks that generate competitive and functional capacities of soil communities will shed light on the ecological and coevolutionary history of sympatric populations, and provide a foundation for more effective management of inhibitory capacities of soil microbial communities.
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93
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Metabolite Cross-Feeding between Rhodococcus ruber YYL and Bacillus cereus MLY1 in the Biodegradation of Tetrahydrofuran under pH Stress. Appl Environ Microbiol 2019; 85:AEM.01196-19. [PMID: 31375492 DOI: 10.1128/aem.01196-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial consortia are among the most basic units in the biodegradation of environmental pollutants. Pollutant-degrading strains frequently encounter different types of environmental stresses and must be able to survive with other bacteria present in the polluted environments. In this study, we proposed a noncontact interaction mode between a tetrahydrofuran (THF)-degrading strain, Rhodococcus ruber YYL, and a non-THF-degrading strain, Bacillus cereus MLY1. The metabolic interaction mechanism between strains YYL and MLY1 was explored through physiological and molecular studies and was further supported by the metabolic response profile of strain YYL, both monocultured and cocultured with strain MLY1 at the optimal pH (pH 8.3) and under pH stress (pH 7.0), through a liquid chromatography-mass spectrometry-based metabolomic analysis. The results suggested that the coculture system resists pH stress in three ways: (i) strain MLY1 utilized acid metabolites and impacted the proportion of glutamine, resulting in an elevated intracellular pH of the system; (ii) strain MLY1 had the ability to degrade intermediates, thus alleviating the product inhibition of strain YYL; and (iii) strain MLY1 produced some essential micronutrients for strain YYL to aid the growth of this strain under pH stress, while strain YYL produced THF degradation intermediates for strain MLY1 as major nutrients. In addition, a metabolite cross-feeding interaction with respect to pollutant biodegradation is discussed.IMPORTANCE Rhodococcus species have been discovered in diverse environmental niches and can degrade numerous recalcitrant toxic pollutants. However, the pollutant degradation efficiency of these strains is severely reduced due to the complexity of environmental conditions and limitations in the growth of the pollutant-degrading microorganism. In our study, Bacillus cereus strain MLY1 exhibited strong stress resistance to adapt to various environments and improved the THF degradation efficiency of Rhodococcus ruber YYL by a metabolic cross-feeding interaction style to relieve the pH stress. These findings suggest that metabolite cross-feeding occurred in a complementary manner, allowing a pollutant-degrading strain to collaborate with a nondegrading strain in the biodegradation of various recalcitrant compounds. The study of metabolic exchanges is crucial to elucidate mechanisms by which degrading and symbiotic bacteria interact to survive environmental stress.
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94
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Miller DP, Fitzsimonds ZR, Lamont RJ. Metabolic Signaling and Spatial Interactions in the Oral Polymicrobial Community. J Dent Res 2019; 98:1308-1314. [PMID: 31356756 DOI: 10.1177/0022034519866440] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Oral supra- and subgingival biofilms are complex communities in which hundreds of bacteria, viruses, and fungi reside and interact. In these social environments, microbes compete and cooperate for resources, such as living space and nutrients. The metabolic activities of bacteria can transform their microenvironment and dynamically influence the fitness and growth of cohabitating organisms. Biofilm communities are temporally and spatially organized largely due to cell-to-cell communication, which promotes synergistic interactions. Metabolic interactions maintain biofilm homeostasis through mutualistic cross-feeding, metabolic syntrophy, and cross-respiration. These interactions include reciprocal metabolite exchanges that promote the growth of physiologically compatible bacteria, processive catabolism of complex substrates, and unidirectional interactions that are globally important for the polymicrobial community. Additionally, oral bacterial interactions can lead to detoxification of oxidative compounds, which will provide protection to the community at large. It has also been established that specific organisms provide terminal electron acceptors to partner species that result in a shift from fermentation to respiration, thus increasing ATP yields and improving fitness. Indeed, many interspecies relationships are multidimensional, and the net outcome can be spatially and temporally dependent. Cross-kingdom interactions also occur as oral yeast are antagonistic to some oral bacteria, while numerous mutualistic interactions contribute to yeast-bacterial colonization, fitness in the oral community, and the pathogenesis of caries. Consideration of this social environment reveals behaviors and phenotypes that are not apparent through the study of microbes in isolation. Here, we provide a comprehensive overview of the metabolic interactions that shape the oral microbial community.
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Affiliation(s)
- D P Miller
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - Z R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
| | - R J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA
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95
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Engineering Synthetic Microbial Communities through a Selective Biofilm Cultivation Device for the Production of Fermented Beverages. Microorganisms 2019; 7:microorganisms7070206. [PMID: 31330825 PMCID: PMC6680646 DOI: 10.3390/microorganisms7070206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022] Open
Abstract
Production of Cambodian rice wine involves complex microbial consortia. Indeed, previous studies focused on traditional microbial starters used for this product revealed that three microbial strains with complementary metabolic activities are required for an effective fermentation, i.e., filamentous fungi (Rhizopus oryzae), yeast (Saccharomycescerevisiae), and lactic acid bacteria (Lactobacillusplantarum). Modulating the ratio between these three key players led to significant differences, not only in terms of ethanol and organic acid production, but also on the profile of volatile compounds, in comparison with natural communities. However, we observed that using an equal ratio of spores/cells of the three microbial strains during inoculation led to flavor profile and ethanol yield close to that obtained through the use of natural communities. Compartmentalization of metabolic tasks through the use of a biofilm cultivation device allows further improvement of the whole fermentation process, notably by increasing the amount of key components of the aroma profile of the fermented beverage (i.e., mainly phenylethyl alcohol, isobutyl alcohol, isoamyl alcohol, and 2-methyl-butanol) and reducing the amount of off-flavor compounds. This study is a step forward in our understanding of interkingdom microbial interactions with strong application potential in food biotechnology.
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96
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Lannes R, Olsson-Francis K, Lopez P, Bapteste E. Carbon Fixation by Marine Ultrasmall Prokaryotes. Genome Biol Evol 2019; 11:1166-1177. [PMID: 30903144 PMCID: PMC6475129 DOI: 10.1093/gbe/evz050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin–Benson–Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood–Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle, have been described. Nano-organisms such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described; and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways was quantified and tested for the presence of all key enzymes in nano-organisms from across the World Ocean. The novel marine ultrasmall prokaryotes were demonstrated to collectively harbor the genes required for carbon fixation, in particular the “energetically efficient” dicarboxylate/4-hydroxybutyrate pathway and the 4-hydroxybutyrate pathway. This contrasted with the known carbon metabolic pathways associated with CPR members in aquifers, where they are described as degraders (Castelle CJ, et al. 2015. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 25(6):690–701; Castelle CJ, et al. 2018. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat Rev Microbiol. 16(10):629–645; Anantharaman K, et al. 2016. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 7:13219.). Our findings suggest that nano-organisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN superphyla are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nano-organisms by future single cell genomics is anticipated.
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Affiliation(s)
- Romain Lannes
- Sorbonne Université, Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystems, The Open University, Milton Keynes, United Kingdom
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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97
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Bernstein DB, Dewhirst FE, Segrè D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife 2019; 8:39733. [PMID: 31194675 PMCID: PMC6609349 DOI: 10.7554/elife.39733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 06/13/2019] [Indexed: 12/18/2022] Open
Abstract
The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.
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Affiliation(s)
- David B Bernstein
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States
| | - Floyd E Dewhirst
- The Forsyth Institute, Cambridge, United States.,Harvard School of Dental Medicine, Boston, United States
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, United States.,Biological Design Center, Boston University, Boston, United States.,Bioinformatics Program, Boston University, Boston, United States.,Department of Biology, Boston University, Boston, United States.,Department of Physics, Boston University, Boston, United States
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98
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Wright RJ, Gibson MI, Christie-Oleza JA. Understanding microbial community dynamics to improve optimal microbiome selection. MICROBIOME 2019; 7:85. [PMID: 31159875 PMCID: PMC6547603 DOI: 10.1186/s40168-019-0702-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown. RESULTS Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms. CONCLUSIONS The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
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99
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Abstract
Study of simplified microbial consortia shows that nitrogen overflow by yeast is a mechanism that supports the stable co-existence of yeasts and lactic acid bacteria.
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Affiliation(s)
- Tatyana Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - James Yi Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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100
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Escudeiro P, Pothier J, Dionisio F, Nogueira T. Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes. mSphere 2019; 4:e00135-19. [PMID: 31043514 PMCID: PMC6495336 DOI: 10.1128/msphere.00135-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 04/11/2019] [Indexed: 01/12/2023] Open
Abstract
Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.
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Affiliation(s)
- Pedro Escudeiro
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Joël Pothier
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Francisco Dionisio
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Nogueira
- cE3c-Centro de Ecologia, Evolução e Alterações Ambientais, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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