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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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Ai J, Yu T, Liu X, Jiang Y, Hao Z, Zhao X, Wang E, Deng Z. Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii. Front Microbiol 2022; 13:1078208. [PMID: 36532429 PMCID: PMC9751200 DOI: 10.3389/fmicb.2022.1078208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.
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Affiliation(s)
- Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaodong Liu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Yingying Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Ziwei Hao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaoyu Zhao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Entao Wang
- , Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenshan Deng
- College of Life Sciences, Yan’an University, Yan’an, China,*Correspondence: Zhenshan Deng,
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Guéneau V, Plateau-Gonthier J, Arnaud L, Piard JC, Castex M, Briandet R. Positive biofilms to guide surface microbial ecology in livestock buildings. Biofilm 2022; 4:100075. [PMID: 35494622 PMCID: PMC9039864 DOI: 10.1016/j.bioflm.2022.100075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 12/12/2022] Open
Abstract
The increase in human consumption of animal proteins implies changes in the management of meat production. This is followed by increasingly restrictive regulations on antimicrobial products such as chemical biocides and antibiotics, used in particular to control pathogens that can spread zoonotic diseases. Aligned with the One Health concept, alternative biological solutions are under development and are starting to be used in animal production. Beneficial bacteria able to form positive biofilms and guide surface microbial ecology to limit microbial pathogen settlement are promising tools that could complement existing biosecurity practices to maintain the hygiene of livestock buildings. Although the benefits of positive biofilms have already been documented, the associated fundamental mechanisms and the rationale of the microbial composition of these new products are still sparce. This review provides an overview of the envisioned modes of action of positive biofilms used on livestock building surfaces and the resulting criteria for the selection of the appropriate microorganisms for this specific application. Limits and advantages of this biosecurity approach are discussed as well as the impact of such practices along the food chain, from farm to fork.
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Affiliation(s)
- Virgile Guéneau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lallemand SAS, 31702, Blagnac, France
| | | | | | - Jean-Christophe Piard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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Zath GK, Sperling RA, Hoffman CW, Bikos DA, Abbasi R, Abate AR, Weitz DA, Chang CB. Rapid parallel generation of a fluorescently barcoded drop library from a microtiter plate using the plate-interfacing parallel encapsulation (PIPE) chip. LAB ON A CHIP 2022; 22:4735-4745. [PMID: 36367139 PMCID: PMC10016142 DOI: 10.1039/d2lc00909a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In drop-based microfluidics, an aqueous sample is partitioned into drops using individual pump sources that drive water and oil into a drop-making device. Parallelization of drop-making devices is necessary to achieve high-throughput screening of multiple experimental conditions, especially in time-sensitive studies. Here, we present the plate-interfacing parallel encapsulation (PIPE) chip, a microfluidic chip designed to generate 50 to 90 μm diameter drops of up to 96 different conditions in parallel by interfacing individual drop makers with a standard 384-well microtiter plate. The PIPE chip is used to generate two types of optically barcoded drop libraries consisting of two-color fluorescent particle combinations: a library of 24 microbead barcodes and a library of 192 quantum dot barcodes. Barcoded combinations in the drop libraries are rapidly measured within a microfluidic device using fluorescence detection and distinct barcoded populations in the fluorescence drop data are identified using DBSCAN data clustering. Signal analysis reveals that particle size defines the source of dominant noise present in the fluorescence intensity distributions of the barcoded drop populations, arising from Poisson loading for microbeads and shot noise for quantum dots. A barcoded population from a drop library is isolated using fluorescence-activated drop sorting, enabling downstream analysis of drop contents. The PIPE chip can improve multiplexed high-throughput assays by enabling simultaneous encapsulation of barcoded samples stored in a microtiter plate and reducing sample preparation time.
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Affiliation(s)
- Geoffrey K Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Ralph A Sperling
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Fraunhofer Institute for Microengineering and Microsystems IMM, Mainz, Germany
| | - Carter W Hoffman
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - Dimitri A Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Reha Abbasi
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - David A Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
| | - Connie B Chang
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
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Chang X, Wei D, Zeng Y, Zhao X, Hu Y, Wu X, Song C, Gong G, Chen H, Yang C, Zhang M, Liu T, Chen W, Yang W. Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean. Front Microbiol 2022; 13:1009689. [PMID: 36386647 PMCID: PMC9643879 DOI: 10.3389/fmicb.2022.1009689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/29/2022] [Indexed: 11/29/2022] Open
Abstract
Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.
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Affiliation(s)
- Xiaoli Chang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dengqin Wei
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Yuhan Zeng
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Xinyu Zhao
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Yu Hu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Xiaoling Wu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Chun Song
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Guoshu Gong
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Huabao Chen
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Chunping Yang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Taiguo Liu
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Wanquan Chen
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
| | - Wenyu Yang
- College of Agronomy and Sichuan Engineering Research Center for Crop Strip Intercropping System, Sichuan Agricultural University, Chengdu, China
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56
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Kose T, Lins TF, Wang J, O’brien AM, Sinton D, Frederickson ME. Accelerated High-throughput Plant Imaging and Phenotyping System.. [DOI: 10.1101/2022.09.28.509964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractThe complex web of interactions in biological communities is an area of study that requires large multifactorial experiments with sufficient statistical power. The use of automated tools can reduce the time and labor associated with experiment setup, data collection, and analysis in experiments aimed at untangling these webs. Here we demonstrate tools for high-throughput experimentation (HTE) in duckweeds, small aquatic plants that are amenable to autonomous experimental preparation and image-based phenotyping. We showcase the abilities of our HTE system in a study with 6,000 experimental units grown across 1,000 different nutrient environments. The use of our automated tools facilitated the collection and analysis of time-resolved growth data, which revealed finer dynamics of plant-microbe interactions across environmental gradients. Altogether, our HTE system can run experiments of up to 11,520 experimental units and can be adapted to studies with other small organisms.
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57
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
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Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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Yu Y, Wen H, Li S, Cao H, Li X, Ma Z, She X, Zhou L, Huang S. Emerging microfluidic technologies for microbiome research. Front Microbiol 2022; 13:906979. [PMID: 36051769 PMCID: PMC9424851 DOI: 10.3389/fmicb.2022.906979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of the microbiome is increasingly prominent. For example, the human microbiome has been proven to be strongly associated with health conditions, while the environmental microbiome is recognized to have a profound influence on agriculture and even the global climate. Furthermore, the microbiome can serve as a fascinating reservoir of genes that encode tremendously valuable compounds for industrial and medical applications. In the past decades, various technologies have been developed to better understand and exploit the microbiome. In particular, microfluidics has demonstrated its strength and prominence in the microbiome research. By taking advantage of microfluidic technologies, inherited shortcomings of traditional methods such as low throughput, labor-consuming, and high-cost are being compensated or bypassed. In this review, we will summarize a broad spectrum of microfluidic technologies that have addressed various needs in the field of microbiome research, as well as the achievements that were enabled by the microfluidics (or technological advances). Finally, how microfluidics overcomes the limitations of conventional methods by technology integration will also be discussed.
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Affiliation(s)
- Yue Yu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Wen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Sihong Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Haojie Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuefei Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhixin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyi She
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
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Recent Progress in the Development of Droplet-based Microfluidic Technologies for Phenotypic Screening using Cell-cell Interactions. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Abstract
Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~105-fold by mineralogy and ~103-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. IMPORTANCE Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.
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Droplet-based methods for tackling antimicrobial resistance. Curr Opin Biotechnol 2022; 76:102755. [PMID: 35841864 DOI: 10.1016/j.copbio.2022.102755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022]
Abstract
Application of droplet-based methods enables (i) faster detection, (ii) increased sensitivity, (iii) characterization of the level of heterogeneity in response to antibiotics by bacterial populations, and (iv) expanded screening of the effectiveness of antibiotic combinations. Hereby, we discuss the key steps and parameters of droplet-based experiments to investigate antimicrobial resistance. We also review recent findings accomplished with these methods and highlight their advantages and capacity to yield new insights into the problem of antimicrobial resistance.
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63
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Ranjbaran M, Verma MS. Microfluidics at the interface of bacteria and fresh produce. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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65
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Ludington WB. Higher-order microbiome interactions and how to find them. Trends Microbiol 2022; 30:618-621. [DOI: 10.1016/j.tim.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
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67
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Tan JY, Saleski TE, Lin XN. The effect of droplet size on syntrophic dynamics in droplet-enabled microbial co-cultivation. PLoS One 2022; 17:e0266282. [PMID: 35358282 PMCID: PMC8970485 DOI: 10.1371/journal.pone.0266282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/17/2022] [Indexed: 11/19/2022] Open
Abstract
Co-cultivation in microfluidic droplets has emerged as a versatile tool for the study of natural and synthetic microbial communities. In particular, the identification and characterization of syntrophic interactions in these communities is attracting increasing interest due to their critical importance for the functioning of environmental and host-associated communities as well as new biotechnological applications. However, one critical parameter in droplet-enabled co-cultivation that has evaded appropriate evaluation is the droplet size. Given the same number of initial cells, a larger droplet size can increase the length scale secreted metabolites must diffuse as well as dilute the initial concentration of cells and exchanged metabolites, impacting the community dynamics. To evaluate the effect of droplet size on a spectrum of syntrophic interactions, we cultivated a synthetic model system consisting of two E. coli auxotrophs, whose interactions could be modulated through supplementation of related amino acids in the medium. Our results demonstrate that the droplet size impacts substantially numerous aspects of the growth of a cross-feeding bi-culture, particularly the growth capacity, maximum specific growth rate, and lag time, depending on the degree of the interaction. This work heavily suggests that one droplet size does not fit all types of interactions; this parameter should be carefully evaluated and chosen in experimental studies that aim to utilize droplet-enabled co-cultivation to characterize or elucidate microbial interactions.
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Affiliation(s)
- James Y. Tan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tatyana E. Saleski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
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68
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Thakku SG, Ackerman CM, Myhrvold C, Bhattacharyya RP, Livny J, Ma P, Gomez GI, Sabeti PC, Blainey PC, Hung DT. Multiplexed detection of bacterial nucleic acids using Cas13 in droplet microarrays. PNAS NEXUS 2022; 1:pgac021. [PMID: 35450424 PMCID: PMC9013781 DOI: 10.1093/pnasnexus/pgac021] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/22/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022]
Abstract
Rapid and accurate diagnosis of infections is fundamental to individual patient care and public health management. Nucleic acid detection methods are critical to this effort, but are limited either in the breadth of pathogens targeted or by the expertise and infrastructure required. We present here a high-throughput system that enables rapid identification of bacterial pathogens, bCARMEN, which utilizes: (1) modular CRISPR-Cas13-based nucleic acid detection with enhanced sensitivity and specificity; and (2) a droplet microfluidic system that enables thousands of simultaneous, spatially multiplexed detection reactions at nanoliter volumes; and (3) a novel preamplification strategy that further enhances sensitivity and specificity. We demonstrate bCARMEN is capable of detecting and discriminating 52 clinically relevant bacterial species and several key antibiotic resistance genes. We further develop a simple proof of principle workflow using stabilized reagents and cell phone camera optical readout, opening up the possibility of a rapid point-of-care multiplexed bacterial pathogen identification and antibiotic susceptibility testing.
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Affiliation(s)
| | | | | | | | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peijun Ma
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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69
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Gopalakrishnappa C, Gowda K, Prabhakara KH, Kuehn S. An ensemble approach to the structure-function problem in microbial communities. iScience 2022; 25:103761. [PMID: 35141504 PMCID: PMC8810406 DOI: 10.1016/j.isci.2022.103761] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.
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Affiliation(s)
| | - Karna Gowda
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Kaumudi H. Prabhakara
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
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70
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Mall A, Kasarlawar S, Saini S. Limited Pairwise Synergistic and Antagonistic Interactions Impart Stability to Microbial Communities. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.648997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the central goals of ecology is to explain and predict coexistence of species. In this context, microbial communities provide a model system where community structure can be studied in environmental niches and in laboratory conditions. A community of microbial population is stabilized by interactions between participating species. However, the nature of these stabilizing interactions has remained largely unknown. Theory and experiments have suggested that communities are stabilized by antagonistic interactions between member species, and destabilized by synergistic interactions. However, experiments have also revealed that a large fraction of all the interactions between species in a community are synergistic in nature. To understand the relative significance of the two types of interactions (synergistic vs. antagonistic) between species, we perform simulations of microbial communities with a small number of participating species using two frameworks—a replicator equation and a Lotka-Volterra framework. Our results demonstrate that synergistic interactions between species play a critical role in maintaining diversity in cultures. These interactions are critical for the ability of the communities to survive perturbations and maintain diversity. We follow up the simulations with quantification of the extent to which synergistic and antagonistic interactions are present in a bacterial community present in a soil sample. Overall, our results show that community stability is largely achieved with the help of synergistic interactions between participating species. However, we perform experiments to demonstrate that antagonistic interactions, in specific circumstances, can also contribute toward community stability.
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71
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Abstract
Individuals are constantly exposed to microbial organisms that may or may not colonize their gut microbiome, and newborn individuals assemble their microbiomes through a number of these acquisition events. Since microbiome composition has been shown to influence host physiology, a mechanistic understanding of community assembly has potentially therapeutic applications. In this paper we study microbiome acquisition in a highly controlled setting using germ-free fruit flies inoculated with specific bacterial species at known abundances. Our approach revealed that acquisition events are stochastic, and the colonization odds of different species in different contexts encode ecological information about interactions. These findings have consequences for microbiome-based therapies like fecal microbiota transplantation that attempt to modify a person’s gut microbiome by deliberately introducing foreign microbes. Observational studies reveal substantial variability in microbiome composition across individuals. Targeted studies in gnotobiotic animals underscore this variability by showing that some bacterial strains colonize deterministically, while others colonize stochastically. While some of this variability can be explained by external factors like environmental, dietary, and genetic differences between individuals, in this paper we show that for the model organism Drosophila melanogaster, interactions between bacteria can affect the microbiome assembly process, contributing to a baseline level of microbiome variability even among isogenic organisms that are identically reared, housed, and fed. In germ-free flies fed known combinations of bacterial species, we find that some species colonize more frequently than others even when fed at the same high concentration. We develop an ecological technique that infers the presence of interactions between bacterial species based on their colonization odds in different contexts, requiring only presence/absence data from two-species experiments. We use a progressive sequence of probabilistic models, in which the colonization of each bacterial species is treated as an independent stochastic process, to reproduce the empirical distributions of colonization outcomes across experiments. We find that incorporating context-dependent interactions substantially improves the performance of the models. Stochastic, context-dependent microbiome assembly underlies clinical therapies like fecal microbiota transplantation and probiotic administration and should inform the design of synthetic fecal transplants and dosing regimes.
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72
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Aranda-Díaz A, Ng KM, Thomsen T, Real-Ramírez I, Dahan D, Dittmar S, Gonzalez CG, Chavez T, Vasquez KS, Nguyen TH, Yu FB, Higginbottom SK, Neff NF, Elias JE, Sonnenburg JL, Huang KC. Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota. Cell Host Microbe 2022; 30:260-272.e5. [PMID: 35051349 PMCID: PMC9082339 DOI: 10.1016/j.chom.2021.12.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.
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Affiliation(s)
- Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Tani Thomsen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susannah Dittmar
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Carlos Gutierrez Gonzalez
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taylor Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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73
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Genomic structure predicts metabolite dynamics in microbial communities. Cell 2022; 185:530-546.e25. [PMID: 35085485 DOI: 10.1016/j.cell.2021.12.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/16/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
Abstract
The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.
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74
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Pierce EC, Dutton RJ. Putting microbial interactions back into community contexts. Curr Opin Microbiol 2022; 65:56-63. [PMID: 34739927 DOI: 10.1016/j.mib.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
Microbial interactions are key aspects of the biology of microbiomes. Recently, there has been a shift in the field towards studying interactions in more representative contexts, whether using multispecies model microbial communities or by looking at interactions in situ. Across diverse microbial systems, these studies have begun to identify common interaction mechanisms. These mechanisms include interactions related to toxic molecules, nutrient competition and cross-feeding, access to metals, signaling pathways, pH changes, and interactions within biofilms. Leveraging technological innovations, many of these studies have used an interdisciplinary approach combining genetic, metabolomic, imaging, and/or microfluidic techniques to gain insight into mechanisms of microbial interactions and into the impact of these interactions on microbiomes.
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Affiliation(s)
- Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, USA.
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75
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Li H, Zhang P, Hsieh K, Wang TH. Combinatorial nanodroplet platform for screening antibiotic combinations. LAB ON A CHIP 2022; 22:621-631. [PMID: 35015012 PMCID: PMC9035339 DOI: 10.1039/d1lc00865j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The emergence and spread of multidrug resistant bacterial strains and concomitant dwindling of effective antibiotics pose worldwide healthcare challenges. To address these challenges, advanced engineering tools are developed to personalize antibiotic treatments by speeding up the diagnostics that is critical to prevent antibiotic misuse and overuse and make full use of existing antibiotics. Meanwhile, it is necessary to investigate novel antibiotic strategies. Recently, repurposing mono antibiotics into combinatorial antibiotic therapies has shown great potential for treatment of bacterial infections. However, widespread adoption of drug combinations has been hindered by the complexity of screening techniques and the cost of reagent consumptions in practice. In this study, we developed a combinatorial nanodroplet platform for automated and high-throughput screening of antibiotic combinations while consuming orders of magnitude lower reagents than the standard microtiter-based screening method. In particular, the proposed platform is capable of creating nanoliter droplets with multiple reagents in an automatic manner, tuning concentrations of each component, performing biochemical assays with high flexibility (e.g., temperature and duration), and achieving detection with high sensitivity. A biochemical assay, based on the reduction of resazurin by the metabolism of bacteria, has been characterized and employed to evaluate the combinatorial effects of the antibiotics of interest. In a pilot study, we successfully screened pairwise combinations between 4 antibiotics for a model Escherichia coli strain.
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Affiliation(s)
- Hui Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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76
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Robustness: linking strain design to viable bioprocesses. Trends Biotechnol 2022; 40:918-931. [PMID: 35120750 DOI: 10.1016/j.tibtech.2022.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/18/2022]
Abstract
Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals. Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions. This limitation arises from a lack of robustness - the ability to maintain a constant phenotype despite the perturbations of such processes. This review describes predictable and stochastic industrial perturbations as well as state-of-the-art technologies to counter process variability. Moreover, we distinguish robustness from tolerance and discuss the potential of single-cell studies for improving system robustness. Finally, we highlight ways of achieving consistent and comparable quantification of robustness that can guide the selection of strains for industrial bioprocesses.
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77
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Zhu X, Wang K, Yan H, Liu C, Zhu X, Chen B. Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:711-731. [PMID: 34985862 DOI: 10.1021/acs.est.1c03899] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.
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Affiliation(s)
- Xiangyu Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Kun Wang
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Huicong Yan
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Congcong Liu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Xiaoying Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
| | - Baoliang Chen
- Department of Environmental Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China
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78
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Slow expanders invade by forming dented fronts in microbial colonies. Proc Natl Acad Sci U S A 2022; 119:2108653119. [PMID: 34983839 PMCID: PMC8740590 DOI: 10.1073/pnas.2108653119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2021] [Indexed: 12/19/2022] Open
Abstract
Living organisms never cease to evolve, so there is a significant interest in predicting and controlling evolution in all branches of life sciences. The most basic question is whether a trait should increase or decrease in a given environment. The answer seems to be trivial for traits such as the growth rate in a bioreactor or the expansion rate of a tumor. Yet, it has been suggested that such traits can decrease, rather than increase, during evolution. Here, we report a mutant that outcompeted the ancestor despite having a slower expansion velocity when in isolation. To explain this observation, we developed and validated a theory that describes spatial competition between organisms with different expansion rates and arbitrary competitive interactions. Most organisms grow in space, whether they are viruses spreading within a host tissue or invasive species colonizing a new continent. Evolution typically selects for higher expansion rates during spatial growth, but it has been suggested that slower expanders can take over under certain conditions. Here, we report an experimental observation of such population dynamics. We demonstrate that mutants that grow slower in isolation nevertheless win in competition, not only when the two types are intermixed, but also when they are spatially segregated into sectors. The latter was thought to be impossible because previous studies focused exclusively on the global competitions mediated by expansion velocities, but overlooked the local competitions at sector boundaries. Local competition, however, can enhance the velocity of either type at the sector boundary and thus alter expansion dynamics. We developed a theory that accounts for both local and global competitions and describes all possible sector shapes. In particular, the theory predicted that a slower on its own, but more competitive, mutant forms a dented V-shaped sector as it takes over the expansion front. Such sectors were indeed observed experimentally, and their shapes matched quantitatively with the theory. In simulations, we further explored several mechanisms that could provide slow expanders with a local competitive advantage and showed that they are all well-described by our theory. Taken together, our results shed light on previously unexplored outcomes of spatial competition and establish a universal framework to understand evolutionary and ecological dynamics in expanding populations.
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79
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Sullam KE, Musa T. Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens. PLANTS 2021; 10:plants10122697. [PMID: 34961168 PMCID: PMC8707103 DOI: 10.3390/plants10122697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.
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80
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Kehe J, Ortiz A, Kulesa A, Gore J, Blainey PC, Friedman J. Positive interactions are common among culturable bacteria. SCIENCE ADVANCES 2021; 7:eabi7159. [PMID: 34739314 PMCID: PMC8570599 DOI: 10.1126/sciadv.abi7159] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/16/2021] [Indexed: 05/19/2023]
Abstract
Interspecies interactions shape the structure and function of microbial communities. In particular, positive, growth-promoting interactions can substantially affect the diversity and productivity of natural and engineered communities. However, the prevalence of positive interactions and the conditions in which they occur are not well understood. To address this knowledge gap, we used kChip, an ultrahigh-throughput coculture platform, to measure 180,408 interactions among 20 soil bacteria across 40 carbon environments. We find that positive interactions, often described to be rare, occur commonly and primarily as parasitisms between strains that differ in their carbon consumption profiles. Notably, nongrowing strains are almost always promoted by strongly growing strains (85%), suggesting a simple positive interaction–mediated approach for cultivation, microbiome engineering, and microbial consortium design.
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Affiliation(s)
- Jared Kehe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anthony Ortiz
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony Kulesa
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul C. Blainey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
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81
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Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc 2021; 16:5030-5082. [PMID: 34635859 PMCID: PMC10824140 DOI: 10.1038/s41596-021-00593-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/16/2021] [Indexed: 02/08/2023]
Abstract
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. This protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
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Affiliation(s)
- Ilija Dukovski
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Djordje Bajić
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jeremy M Chacón
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Michael Quintin
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Snorre Sulheim
- Bioinformatics Program, Boston University, Boston, MA, USA
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Alan R Pacheco
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - David B Bernstein
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kirill S Korolev
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Physics, Boston University, Boston, MA, USA
| | - Alvaro Sanchez
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - William R Harcombe
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
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82
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Ha NS, de Raad M, Han LZ, Golini A, Petzold CJ, Northen TR. Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology. RSC Chem Biol 2021; 2:1331-1351. [PMID: 34704041 PMCID: PMC8496484 DOI: 10.1039/d1cb00112d] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.
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Affiliation(s)
- Noel S Ha
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - La Zhen Han
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Amber Golini
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Trent R Northen
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
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83
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van Tatenhove-Pel RJ, de Groot DH, Bisseswar AS, Teusink B, Bachmann H. Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth. THE ISME JOURNAL 2021; 15:3050-3061. [PMID: 33953364 PMCID: PMC8443577 DOI: 10.1038/s41396-021-00986-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/29/2021] [Accepted: 04/09/2021] [Indexed: 02/01/2023]
Abstract
As natural selection acts on individual organisms the evolution of costly cooperation between microorganisms is an intriguing phenomenon. Introduction of spatial structure to privatize exchanged molecules can explain the evolution of cooperation. However, in many natural systems cells can also grow to low cell concentrations in the absence of these exchanged molecules, thus showing "cooperation-independent background growth". We here serially propagated a synthetic cross-feeding consortium of lactococci in the droplets of a water-in-oil emulsion, essentially mimicking group selection with varying founder population sizes. The results show that when the growth of cheaters completely depends on cooperators, cooperators outcompete cheaters. However, cheaters outcompete cooperators when they can independently grow to only ten percent of the consortium carrying capacity. This result is the consequence of a probabilistic effect, as low founder population sizes in droplets decrease the frequency of cooperator co-localization. Cooperator-enrichment can be recovered by increasing the founder population size in droplets to intermediate values. Together with mathematical modelling our results suggest that co-localization probabilities in a spatially structured environment leave a small window of opportunity for the evolution of cooperation between organisms that do not benefit from their cooperative trait when in isolation or form multispecies aggregates.
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Affiliation(s)
- Rinke J. van Tatenhove-Pel
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands ,grid.5292.c0000 0001 2097 4740Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands
| | - Daan H. de Groot
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Anjani S. Bisseswar
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Bas Teusink
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands
| | - Herwig Bachmann
- grid.12380.380000 0004 1754 9227Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, Amsterdam, The Netherlands ,grid.419921.60000 0004 0588 7915NIZO Food Research, Kernhemseweg 2, Ede, The Netherlands
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84
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Ou Y, Cao S, Zhang J, Dong W, Yang Z, Yu Z. Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology. Trends Analyt Chem 2021; 143:116333. [PMID: 34720276 PMCID: PMC8547957 DOI: 10.1016/j.trac.2021.116333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.
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Affiliation(s)
- Yangteng Ou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shixiang Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Jing Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ziyi Yu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
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85
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Gupta G, Ndiaye A, Filteau M. Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions. Front Microbiol 2021; 12:700752. [PMID: 34646243 PMCID: PMC8503676 DOI: 10.3389/fmicb.2021.700752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/31/2021] [Indexed: 12/27/2022] Open
Abstract
Microorganisms are a fundamental part of virtually every ecosystem on earth. Understanding how collectively they interact, assemble, and function as communities has become a prevalent topic both in fundamental and applied research. Owing to multiple advances in technology, answering questions at the microbial system or network level is now within our grasp. To map and characterize microbial interaction networks, numerous computational approaches have been developed; however, experimentally validating microbial interactions is no trivial task. Microbial interactions are context-dependent, and their complex nature can result in an array of outcomes, not only in terms of fitness or growth, but also in other relevant functions and phenotypes. Thus, approaches to experimentally capture microbial interactions involve a combination of culture methods and phenotypic or functional characterization methods. Here, through our perspective of food microbiologists, we highlight the breadth of innovative and promising experimental strategies for their potential to capture the different dimensions of microbial interactions and their high-throughput application to answer the question; are microbial interaction patterns or network architecture similar along different contextual scales? We further discuss the experimental approaches used to build various types of networks and study their architecture in the context of cell biology and how they translate at the level of microbial ecosystem.
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Affiliation(s)
- Gunjan Gupta
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Amadou Ndiaye
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Marie Filteau
- Département des Sciences des aliments, Université Laval, Québec, QC, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels (INAF), Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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86
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Abstract
Recent human activity has profoundly transformed Earth biomes on a scale and at rates that are unprecedented. Given the central role of symbioses in ecosystem processes, functions, and services throughout the Earth biosphere, the impacts of human-driven change on symbioses are critical to understand. Symbioses are not merely collections of organisms, but co-evolved partners that arise from the synergistic combination and action of different genetic programs. They function with varying degrees of permanence and selection as emergent units with substantial potential for combinatorial and evolutionary innovation in both structure and function. Following an articulation of operational definitions of symbiosis and related concepts and characteristics of the Anthropocene, we outline a basic typology of anthropogenic change (AC) and a conceptual framework for how AC might mechanistically impact symbioses with select case examples to highlight our perspective. We discuss surprising connections between symbiosis and the Anthropocene, suggesting ways in which new symbioses could arise due to AC, how symbioses could be agents of ecosystem change, and how symbioses, broadly defined, of humans and "farmed" organisms may have launched the Anthropocene. We conclude with reflections on the robustness of symbioses to AC and our perspective on the importance of symbioses as ecosystem keystones and the need to tackle anthropogenic challenges as wise and humble stewards embedded within the system.
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Affiliation(s)
- Erik F. Y. Hom
- Department of Biology and Center for Biodiversity and Conservation Research, University of Mississippi, University, MS 38677 USA
| | - Alexandra S. Penn
- Department of Sociology and Centre for Evaluation of Complexity Across the Nexus, University of Surrey, Guildford, Surrey, GU2 7XH UK
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87
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Hu R, Zhao H, Xu X, Wang Z, Yu K, Shu L, Yan Q, Wu B, Mo C, He Z, Wang C. Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities. ENVIRONMENT INTERNATIONAL 2021; 154:106560. [PMID: 33866059 DOI: 10.1016/j.envint.2021.106560] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/15/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.
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Affiliation(s)
- Ruiwen Hu
- 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
| | - Haiming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xihui Xu
- Department of Microbiology, Key Laboratory of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar 161006, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen 518055, China
| | - Longfei Shu
- 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
| | - Qingyun Yan
- 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
| | - Bo Wu
- 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
| | - Cehui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - 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; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Cheng Wang
- 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.
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88
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Abstract
Microbial communities (microbiomes) have been harnessed in biotechnology applications such as wastewater treatment and bioremediation for over a century. Traditionally, engineering approaches have focused on shaping the environment to steer microbiome function versus direct manipulation of the microbiome's metabolic network. While these selection-based approaches have proven to be invaluable for guiding bioprocess engineering, they do not enable the precise manipulation and control of microbiomes required for unlocking their full potential. Over the past 2 decades, systems biology has revolutionized our understanding of the metabolic networks driving microbiome processes, and more recently genetic engineering tools have started to emerge for nonmodel microorganisms and microbiomes. In this commentary, I discuss how systems biology approaches are being used to generate actionable understanding of microbiome functions in engineered ecosystems. I also highlight how integrating synthetic biology, automation, and machine learning can accelerate microbiome engineering to meet the sustainability challenges of the future.
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Affiliation(s)
- Christopher E Lawson
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
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89
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Lindsay RJ, Jepson A, Butt L, Holder PJ, Smug BJ, Gudelj I. Would that it were so simple: Interactions between multiple traits undermine classical single-trait-based predictions of microbial community function and evolution. Ecol Lett 2021; 24:2775-2795. [PMID: 34453399 DOI: 10.1111/ele.13861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/11/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022]
Abstract
Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under consideration, such as public good production and resistance to antibiotics or predation, are often assumed to act in isolation. Yet, in reality, multiple traits frequently interact, which can lead to unexpected and undesired outcomes for the health of macroorganisms and ecosystem functioning. This is because many predictions generated in a single-trait context aimed at promoting diversity, reducing virulence or controlling antibiotic resistance can fail for systems where multiple traits interact. Here, we provide a much needed discussion and synthesis of the most recent research to reveal the widespread and diverse nature of multi-trait interactions and their consequences for predicting and controlling microbial community dynamics. Importantly, we argue that synthetic microbial communities and multi-trait mathematical models are powerful tools for managing the beneficial and detrimental impacts of microbial communities, such that past mistakes, like those made regarding the stewardship of antimicrobials, are not repeated.
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Affiliation(s)
- Richard J Lindsay
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Alys Jepson
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Lisa Butt
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Philippa J Holder
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ivana Gudelj
- Biosciences and Living Systems Institute, University of Exeter, Exeter, UK
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90
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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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91
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Leggieri PA, Liu Y, Hayes M, Connors B, Seppälä S, O'Malley MA, Venturelli OS. Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. Annu Rev Biomed Eng 2021; 23:169-201. [PMID: 33781078 PMCID: PMC8277735 DOI: 10.1146/annurev-bioeng-082120-022836] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. The spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review, we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.
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Affiliation(s)
- Patrick A Leggieri
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Yiyi Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Madeline Hayes
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Bryce Connors
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA;
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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92
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Zhu M, Tse MW, Weller J, Chen J, Blainey PC. The future of antibiotics begins with discovering new combinations. Ann N Y Acad Sci 2021; 1496:82-96. [PMID: 34212403 PMCID: PMC8290516 DOI: 10.1111/nyas.14649] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
Antibiotic resistance is a worldwide and growing clinical problem. With limited drug development in the antibacterial space, combination therapy has emerged as a promising strategy to combat multidrug-resistant bacteria. Antibacterial combinations can improve antibiotic efficacy and suppress antibacterial resistance through independent, synergistic, or even antagonistic activities. Combination therapies are famously used to treat viral and mycobacterial infections and cancer. However, antibacterial combinations are only now emerging as a common treatment strategy for other bacterial infections owing to challenges in their discovery, development, regulatory approval, and commercial/clinical deployment. Here, we focus on discovery-where the sheer scale of combinatorial chemical spaces represents a significant challenge-and discuss how combination therapy can impact the treatment of bacterial infections. Despite these challenges, recent advancements, including new in silico methods, theoretical frameworks, and microfluidic platforms, are poised to identify the new and efficacious antibacterial combinations needed to revitalize the antibacterial drug pipeline.
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Affiliation(s)
- Meilin Zhu
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Megan W. Tse
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Juliane Weller
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
| | - Julie Chen
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
- Microbiology Graduate ProgramMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Paul C. Blainey
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMassachusetts
- Broad Institute of Massachusetts Institute of Technology and HarvardCambridgeMassachusetts
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of TechnologyCambridgeMassachusetts
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93
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Ortiz A, Vega NM, Ratzke C, Gore J. Interspecies bacterial competition regulates community assembly in the C. elegans intestine. THE ISME JOURNAL 2021; 15:2131-2145. [PMID: 33589765 PMCID: PMC8245486 DOI: 10.1038/s41396-021-00910-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 01/31/2023]
Abstract
From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host-microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species' taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host-microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.
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Affiliation(s)
- Anthony Ortiz
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Nicole M. Vega
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.189967.80000 0001 0941 6502Present Address: Department of Biology, Emory University, Atlanta, GA USA
| | - Christoph Ratzke
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.10392.390000 0001 2190 1447Present Address: Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Cluster of Excellence ‘CMFI’, University of Tübingen, Tübingen, Germany
| | - Jeff Gore
- grid.116068.80000 0001 2341 2786Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA USA
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94
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Pacheco AR, Segrè D. An evolutionary algorithm for designing microbial communities via environmental modification. J R Soc Interface 2021; 18:20210348. [PMID: 34157894 PMCID: PMC8220269 DOI: 10.1098/rsif.2021.0348] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.
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Affiliation(s)
- Alan R Pacheco
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Daniel Segrè
- Graduate Program in Bioinformatics and Biological Design Center, Boston University, Boston, MA 02215, USA.,Department of Biology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Department of Physics, Boston University, Boston, MA 02215, USA
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95
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Coexistence holes characterize the assembly and disassembly of multispecies systems. Nat Ecol Evol 2021; 5:1091-1101. [PMID: 34045718 DOI: 10.1038/s41559-021-01462-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/07/2021] [Indexed: 11/08/2022]
Abstract
A central goal of ecological research has been to understand the limits on the maximum number of species that can coexist under given constraints. However, we know little about the assembly and disassembly processes under which a community can reach such a maximum number, or whether this number is in fact attainable in practice. This limitation is partly due to the challenge of performing experimental work and partly due to the lack of a formalism under which one can systematically study such processes. Here, we introduce a formalism based on algebraic topology and homology theory to study the space of species coexistence formed by a given pool of species. We show that this space is characterized by ubiquitous discontinuities that we call coexistence holes (that is, empty spaces surrounded by filled space). Using theoretical and experimental systems, we provide direct evidence showing that these coexistence holes do not occur arbitrarily-their diversity is constrained by the internal structure of species interactions and their frequency can be explained by the external factors acting on these systems. Our work suggests that the assembly and disassembly of ecological systems is a discontinuous process that tends to obey regularities.
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96
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Ankrah NYD, Barker BE, Song J, Wu C, McMullen JG, Douglas AE. Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. mSystems 2021. [PMID: 33947801 DOI: 10.1101/2021.01.20.427455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition, and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that, in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle, including 2-oxoglutarate and succinate, are produced at high flux and cross-fed between bacterial taxa, suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.IMPORTANCE Drosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila This revealed that metabolic interactions between Drosophila gut bacterial taxa are highly dynamic and influenced by cooccurring bacteria and nutrient availability. Our results generate testable hypotheses about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.
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Affiliation(s)
- Nana Y D Ankrah
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Brandon E Barker
- Center for Advanced Computing, Cornell University, Ithaca, New York, USA
| | - Joan Song
- School of Electrical and Computer Engineering, Cornell University, Ithaca, New York, USA
| | - Cindy Wu
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - John G McMullen
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, New York, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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97
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Ankrah NYD, Barker BE, Song J, Wu C, McMullen JG, Douglas AE. Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. mSystems 2021; 6:e01369-20. [PMID: 33947801 PMCID: PMC8269265 DOI: 10.1128/msystems.01369-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/01/2021] [Indexed: 12/28/2022] Open
Abstract
An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition, and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that, in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle, including 2-oxoglutarate and succinate, are produced at high flux and cross-fed between bacterial taxa, suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.IMPORTANCE Drosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila This revealed that metabolic interactions between Drosophila gut bacterial taxa are highly dynamic and influenced by cooccurring bacteria and nutrient availability. Our results generate testable hypotheses about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.
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Affiliation(s)
- Nana Y D Ankrah
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Brandon E Barker
- Center for Advanced Computing, Cornell University, Ithaca, New York, USA
| | - Joan Song
- School of Electrical and Computer Engineering, Cornell University, Ithaca, New York, USA
| | - Cindy Wu
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - John G McMullen
- Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, New York, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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98
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Yin C, Casa Vargas JM, Schlatter DC, Hagerty CH, Hulbert SH, Paulitz TC. Rhizosphere community selection reveals bacteria associated with reduced root disease. MICROBIOME 2021; 9:86. [PMID: 33836842 PMCID: PMC8035742 DOI: 10.1186/s40168-020-00997-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/29/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. RESULTS In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. CONCLUSIONS Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity. Video Abstract.
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Affiliation(s)
- Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Juan M Casa Vargas
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Daniel C Schlatter
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA
| | - Christina H Hagerty
- Columbia Basin Agricultural Research Center, Oregon State University, Adams, OR, 97810, USA
| | - Scot H Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Timothy C Paulitz
- USDA-ARS, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman, WA, 99164-6430, USA.
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99
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Estrela S, Sánchez Á, Rebolleda-Gómez M. Multi-Replicated Enrichment Communities as a Model System in Microbial Ecology. Front Microbiol 2021; 12:657467. [PMID: 33897672 PMCID: PMC8062719 DOI: 10.3389/fmicb.2021.657467] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Recent advances in robotics and affordable genomic sequencing technologies have made it possible to establish and quantitatively track the assembly of enrichment communities in high-throughput. By conducting community assembly experiments in up to thousands of synthetic habitats, where the extrinsic sources of variation among replicates can be controlled, we can now study the reproducibility and predictability of microbial community assembly at different levels of organization, and its relationship with nutrient composition and other ecological drivers. Through a dialog with mathematical models, high-throughput enrichment communities are bringing us closer to the goal of developing a quantitative predictive theory of microbial community assembly. In this short review, we present an overview of recent research on this growing field, highlighting the connection between theory and experiments and suggesting directions for future work.
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Affiliation(s)
- Sylvie Estrela
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
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100
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Pozo MJ, Zabalgogeazcoa I, Vazquez de Aldana BR, Martinez-Medina A. Untapping the potential of plant mycobiomes for applications in agriculture. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102034. [PMID: 33827007 DOI: 10.1016/j.pbi.2021.102034] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 05/20/2023]
Abstract
Plant-fungal interactions are widespread in nature, and their multiple benefits for plant growth and health have been amply demonstrated. Endophytic and epiphytic fungi can significantly increase plant resilience, improving plant nutrition, stress tolerance and defence. Although some of these interactions have been known for decades, the relevance of the plant mycobiome within the plant microbiome has been largely underestimated. Our limited knowledge of fungal biology and their interactions with plants in the broader phytobiome context has hampered the development of optimal biotechnological applications in agrosystems and natural ecosystems. Exciting recent technical and knowledge advances in the context of molecular and systems biology open a plethora of opportunities for developing this field of research.
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Affiliation(s)
- Maria J Pozo
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain.
| | - Iñigo Zabalgogeazcoa
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Beatriz R Vazquez de Aldana
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
| | - Ainhoa Martinez-Medina
- Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC, Salamanca, Spain
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