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Reese AT, Cho EH, Klitzman B, Nichols SP, Wisniewski NA, Villa MM, Durand HK, Jiang S, Midani FS, Nimmagadda SN, O'Connell TM, Wright JP, Deshusses MA, David LA. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLife 2018; 7:35987. [PMID: 29916366 PMCID: PMC6008055 DOI: 10.7554/elife.35987] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/26/2018] [Indexed: 12/18/2022] Open
Abstract
How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. The gut is home to a large and diverse community of bacteria and other microbes, known as the gut microbiota. The makeup of this community is important for the health of both the host and its residents. For instance, many gut bacteria help to digest food or keep disease-causing bacteria in check. In return, the host provides them with nutrients. When this balance is disturbed, the host is exposed to risks such as infections. In particular, treatments with antibiotics that kill gut bacteria can lead to side effects like diarrhea, because the gut becomes recolonized with harmful bacteria including Clostridium difficile and Salmonella. Reese et al. have now investigated what happens to the gut environment after antibiotic treatment and how the gut microbiota recovers. Mice treated with broad-spectrum antibiotics showed an increase in the “redox potential” of their gut environment. Redox potential captures a number of measures of the chemical makeup of an environment, and provides an estimate for how efficiently some bacteria in that environment can grow. Some of the change in redox potential came from the host’s own immune system releasing chemicals as it reacted to the effects of the treatment. However, Reese et al. found that treating gut bacteria in an artificial gut – which has no immune system – also increased the redox potential. This experiment suggests that bacteria actively shape their chemical environment in the gut. After the treatment, bacteria that thrive under high redox potentials, which include some disease-causing species, recovered first and fastest. This, in turn, helped to bring redox potential back to how it was before the treatment. Although the gut’s chemical environment recovered, some bacterial species were wiped out by the antibiotic treatment. The microbiota only returned to its previous state when the treated mice were housed together with non-treated mice. This was expected because mice that live together commonly exchange microbes, for instance by eating each other’s feces, and the treated mice received new species to replenish their microbiota. These findings are important because they show that the chemical environment shapes and is shaped by the bacterial communities in the gut. Future research may investigate if altering redox potential in the gut could help to keep the microbiota healthier in infections and diseases of the digestive tract.
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Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, United States.,Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Eugenia H Cho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
| | - Bruce Klitzman
- Department of Surgery, Duke University Medical Center, Durham, United States
| | | | | | - Max M Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Firas S Midani
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
| | - Sai N Nimmagadda
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Thomas M O'Connell
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, United States
| | - Justin P Wright
- Department of Biology, Duke University, Durham, United States
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, United States
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States.,Program in Computational Biology and Bioinformatics, Duke University, Durham, United States.,Department of Biomedical Engineering, Duke University, Durham, United States.,Center for Genomic and Computational Biology, Duke University, Durham, United States
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52
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Yang Y, Dou Y, An S. Testing association between soil bacterial diversity and soil carbon storage on the Loess Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 626:48-58. [PMID: 29335174 DOI: 10.1016/j.scitotenv.2018.01.081] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 12/20/2017] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
Bacteria are widely distributed and play an important role in soil carbon (C) cycling. The impact of soil bacterial diversity on soil C storage has been well established, yet little is known about the underlying mechanisms and the interactions among them. Here, we examined the association between soil bacterial diversity and soil C storage in relation to vegetation restoration on the Loess Plateau. The dominant phyla among land use types (artificial forest, Af; natural shrubland, Ns; artificial grassland, Ag; natural grassland, Ng; slope cropland, Sc) were Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria, which transited from Acidobacteria-dominant to Actinobacteria-dominant community due to vegetation restoration. Soil C storage and the Shannon diversity index of soil bacterial community (HBacteria) showed the order Ns > Ng > Af > Ag > Sc, whereas no significant difference was found in Good's coverage (p > .05). Further, a strong relationship was observed between the relative abundance of dominant bacterial groups and soil C storage (p < .05). Additionally, soil bacterial diversity was closely related to soil C storage based on the structural equation model (SEM) and generalized additive models (GAMs). Specifically, soil C storage had the largest deterministic effects, explaining >70% of the variation and suggesting a strong association between soil C storage and soil bacterial diversity. Overall, we propose that further studies are necessary with a focus on the soil bacterial groups with specific functions in relation to soil C storage on the Loess Plateau.
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Affiliation(s)
- Yang Yang
- College of Natural Resource and Environment, Northwest A&F University, Yangling 712100, China
| | - Yanxing Dou
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China
| | - Shaoshan An
- College of Natural Resource and Environment, Northwest A&F University, Yangling 712100, China; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling 712100, China.
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53
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Wu SH, Huang BH, Huang CL, Li G, Liao PC. The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions. MICROBIAL ECOLOGY 2018; 75:434-446. [PMID: 28765980 DOI: 10.1007/s00248-017-1050-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.
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Affiliation(s)
- Shu-Hong Wu
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Gang Li
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan.
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54
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Liu S, Wang H, Deng Y, Tian P, Wang Q. Forest conversion induces seasonal variation in microbial β-diversity. Environ Microbiol 2018; 20:111-123. [DOI: 10.1111/1462-2920.14017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Shengen Liu
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Hang Wang
- National Plateau Wetlands Research Center; Southwest Forestry University; Kunming 650224 China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Science; Chinese Academy of Sciences; Beijing 100085 China
| | - Peng Tian
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
- University of Chinese Academy of Sciences; Beijing 100049 People's Republic of China
| | - Qingkui Wang
- CAS Key Laboratory of Forest Ecology and Management; Institute of Applied Ecology, Huitong Experimental Station of Forest Ecology; Shenyang 110164 People's Republic of China
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55
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Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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56
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Zhou J, Ning D. Stochastic Community Assembly: Does It Matter in Microbial Ecology? Microbiol Mol Biol Rev 2017. [PMID: 29021219 DOI: 10.1128/mmbr] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.
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Affiliation(s)
- Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Daliang Ning
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Science, University of Oklahoma, Norman, Oklahoma, USA
- Consolidated Core Laboratory, University of Oklahoma, Norman, Oklahoma, USA
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57
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Lin Q, De Vrieze J, Li C, Li J, Li J, Yao M, Hedenec P, Li H, Li T, Rui J, Frouz J, Li X. Temperature regulates deterministic processes and the succession of microbial interactions in anaerobic digestion process. WATER RESEARCH 2017; 123:134-143. [PMID: 28662395 DOI: 10.1016/j.watres.2017.06.051] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Temperature plays crucial roles in microbial interactions that affect the stability and performance of anaerobic digestion. In this study, the microbial interactions and their succession in the anaerobic digestion process were investigated at three levels, represented by (1) present and (2) active micro-organisms, and (3) gene expressions under a temperature gradient from 25 to 55 °C. Network topological features indicated a global variation in microbial interactions at different temperatures. The variations of microbial interactions in terms of network modularity and deterministic processes based on topological features, corresponded well with the variations of methane productions, but not with temperatures. A common successional pattern of microbial interactions was observed at different temperatures, which showed that both deterministic processes and network modularity increased over time during the digestion process. It was concluded that the increase in temperature-mediated network modularity and deterministic processes on shaping the microbial interactions improved the stability and efficiency of anaerobic digestion process.
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Affiliation(s)
- Qiang Lin
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China; Institute of Soil Biology, Czech Academy of Sciences, Na Sádkách 7, CZ37005, České Budějovice, Czech Republic
| | - Jo De Vrieze
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - Chaonan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jiaying Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jiabao Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Minjie Yao
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Petr Hedenec
- Institute of Soil Biology, Czech Academy of Sciences, Na Sádkách 7, CZ37005, České Budějovice, Czech Republic
| | - Huan Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Tongtong Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junpeng Rui
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jan Frouz
- Institute of Soil Biology, Czech Academy of Sciences, Na Sádkách 7, CZ37005, České Budějovice, Czech Republic.
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, CAS, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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58
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Abstract
Succession and community assembly research overlap in many respects, such as through their focus on how ecological processes like dispersal, environmental filters, and biotic interactions influence community structure. Indeed, many recent advances have been made by successional studies that draw on modern analytical techniques introduced by contemporary community assembly studies. However, community assembly studies generally lack a temporal perspective, both on how the forces structuring communities might change over time and on how historical contingency (e.g. priority effects and legacy effects) and complex transitions (e.g. threshold effects) might alter community trajectories. We believe a full understanding of the complex interacting processes that shape community dynamics across large temporal scales can best be achieved by combining concepts, tools, and study systems into an integrated conceptual framework that draws upon both succession and community assembly theory.
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Affiliation(s)
- Cynthia Chang
- Division of Biology, School of STEM, University of Washington-Bothell, Bothell, WA, USA
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59
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Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EAG, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. Front Microbiol 2016; 7:579. [PMID: 27199914 PMCID: PMC4842900 DOI: 10.3389/fmicb.2016.00579] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/08/2016] [Indexed: 01/19/2023] Open
Abstract
How soil microbial communities contrast with respect to taxonomic and functional composition within and between ecosystems remains an unresolved question that is central to predicting how global anthropogenic change will affect soil functioning and services. In particular, it remains unclear how small-scale observations of soil communities based on the typical volume sampled (1-2 g) are generalizable to ecosystem-scale responses and processes. This is especially relevant for remote, northern latitude soils, which are challenging to sample and are also thought to be more vulnerable to climate change compared to temperate soils. Here, we employed well-replicated shotgun metagenome and 16S rRNA gene amplicon sequencing to characterize community composition and metabolic potential in Alaskan tundra soils, combining our own datasets with those publically available from distant tundra and temperate grassland and agriculture habitats. We found that the abundance of many taxa and metabolic functions differed substantially between tundra soil metagenomes relative to those from temperate soils, and that a high degree of OTU-sharing exists between tundra locations. Tundra soils were an order of magnitude less complex than their temperate counterparts, allowing for near-complete coverage of microbial community richness (~92% breadth) by sequencing, and the recovery of 27 high-quality, almost complete (>80% completeness) population bins. These population bins, collectively, made up to ~10% of the metagenomic datasets, and represented diverse taxonomic groups and metabolic lifestyles tuned toward sulfur cycling, hydrogen metabolism, methanotrophy, and organic matter oxidation. Several population bins, including members of Acidobacteria, Actinobacteria, and Proteobacteria, were also present in geographically distant (~100-530 km apart) tundra habitats (full genome representation and up to 99.6% genome-derived average nucleotide identity). Collectively, our results revealed that Alaska tundra microbial communities are less diverse and more homogenous across spatial scales than previously anticipated, and provided DNA sequences of abundant populations and genes that would be relevant for future studies of the effects of environmental change on tundra ecosystems.
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Affiliation(s)
- Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta GA, USA
| | - Luis M Rodriguez-R
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, AtlantaGA, USA; School of Biology, Georgia Institute of Technology, AtlantaGA, USA
| | - Chengwei Luo
- Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, Atlanta GA, USA
| | - Mengting M Yuan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - Edward A G Schuur
- Department of Biological Sciences, Northern Arizona University, Flagstaff AZ, USA
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman OK, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing MI, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, NormanOK, USA; Earth Science Division, Lawrence Berkeley National Laboratory, BerkeleyCA, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, AtlantaGA, USA; Center for Bioinformatics and Computational Genomics, Georgia Institute of Technology, AtlantaGA, USA; School of Biology, Georgia Institute of Technology, AtlantaGA, USA
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