1
|
Páez-Watson T, van Loosdrecht MCM, Wahl SA. From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake. WATER RESEARCH 2024; 250:121028. [PMID: 38128304 DOI: 10.1016/j.watres.2023.121028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/06/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.
Collapse
Affiliation(s)
- Timothy Páez-Watson
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | | | - S Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| |
Collapse
|
2
|
Walls AW, Rosenthal AZ. Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing. Transcription 2024; 15:48-62. [PMID: 38532542 DOI: 10.1080/21541264.2024.2334110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution.
Collapse
Affiliation(s)
- Alex W Walls
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Adam Z Rosenthal
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
3
|
Deutschmann IM, Delage E, Giner CR, Sebastián M, Poulain J, Arístegui J, Duarte CM, Acinas SG, Massana R, Gasol JM, Eveillard D, Chaffron S, Logares R. Disentangling microbial networks across pelagic zones in the tropical and subtropical global ocean. Nat Commun 2024; 15:126. [PMID: 38168083 PMCID: PMC10762198 DOI: 10.1038/s41467-023-44550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Microbial interactions are vital in maintaining ocean ecosystem function, yet their dynamic nature and complexity remain largely unexplored. Here, we use association networks to investigate possible ecological interactions in the marine microbiome among archaea, bacteria, and picoeukaryotes throughout different depths and geographical regions of the tropical and subtropical global ocean. Our findings reveal that potential microbial interactions change with depth and geographical scale, exhibiting highly heterogeneous distributions. A few potential interactions were global, meaning they occurred across regions at the same depth, while 11-36% were regional within specific depths. The bathypelagic zone had the lowest proportion of global associations, and regional associations increased with depth. Moreover, we observed that most surface water associations do not persist in deeper ocean layers despite microbial vertical dispersal. Our work contributes to a deeper understanding of the tropical and subtropical global ocean interactome, which is essential for addressing the challenges posed by global change.
Collapse
Affiliation(s)
| | - Erwan Delage
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | | | | | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Javier Arístegui
- Instituto de Oceanografía y Cambio Global, IOCAG, Universidad de Las Palmas de Gran Canaria, ULPGC, Gran Canaria, Spain
| | - Carlos M Duarte
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal, Saudi Arabia
| | | | - Ramon Massana
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Josep M Gasol
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Damien Eveillard
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Samuel Chaffron
- Nantes Université, CNRS UMR 6004, LS2N, F-44000, Nantes, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain.
| |
Collapse
|
4
|
Gonçalves OS, Creevey CJ, Santana MF. Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. ENVIRONMENTAL MICROBIOME 2023; 18:81. [PMID: 37974247 PMCID: PMC10655421 DOI: 10.1186/s40793-023-00536-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants. RESULTS We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla. CONCLUSION Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.
Collapse
Affiliation(s)
- Osiel S Gonçalves
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Mateus F Santana
- Grupo de Genômica Eco-evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
| |
Collapse
|
5
|
Hellal J, Barthelmebs L, Bérard A, Cébron A, Cheloni G, Colas S, Cravo-Laureau C, De Clerck C, Gallois N, Hery M, Martin-Laurent F, Martins J, Morin S, Palacios C, Pesce S, Richaume A, Vuilleumier S. Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges. FEMS Microbiol Ecol 2023; 99:fiad102. [PMID: 37669892 PMCID: PMC10516372 DOI: 10.1093/femsec/fiad102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.
Collapse
Affiliation(s)
| | - Lise Barthelmebs
- Université de Perpignan Via Domitia, Biocapteurs – Analyse-Environnement, Perpignan, France
- Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Annette Bérard
- UMR EMMAH INRAE/AU – équipe SWIFT, 228, route de l'Aérodrome, 84914 Avignon Cedex 9, France
| | | | - Giulia Cheloni
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Simon Colas
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro-Bio Tech (Liege University), Passage des Déportés 2, 5030 Gembloux, Belgium
| | | | - Marina Hery
- HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Fabrice Martin-Laurent
- Institut Agro Dijon, INRAE, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie, 21065 Dijon, France
| | - Jean Martins
- IGE, UMR 5001, Université Grenoble Alpes, CNRS, G-INP, INRAE, IRD Grenoble, France
| | | | - Carmen Palacios
- Université de Perpignan Via Domitia, CEFREM, F-66860 Perpignan, France
- CNRS, CEFREM, UMR5110, F-66860 Perpignan, France
| | | | - Agnès Richaume
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5557, Ecologie Microbienne, Villeurbanne, France
| | | |
Collapse
|
6
|
Schlechter RO, Kear EJ, Bernach M, Remus DM, Remus-Emsermann MNP. Metabolic resource overlap impacts competition among phyllosphere bacteria. THE ISME JOURNAL 2023; 17:1445-1454. [PMID: 37355740 PMCID: PMC10432529 DOI: 10.1038/s41396-023-01459-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
The phyllosphere is densely colonised by microbial communities, despite sparse and heterogeneously distributed resources. The limitation of resources is expected to drive bacterial competition resulting in exclusion or coexistence based on fitness differences and resource overlap between individual colonisers. We studied the impact of resource competition by determining the effects of different bacterial colonisers on the growth of the model epiphyte Pantoea eucalypti 299R (Pe299R). Resource overlap was predicted based on genome-scale metabolic modelling. By combining results of metabolic modelling and pairwise competitions in the Arabidopsis thaliana phyllosphere and in vitro, we found that ten resources sufficed to explain fitness of Pe299R. An effect of both resource overlap and phylogenetic relationships was found on competition outcomes in vitro as well as in the phyllosphere. However, effects of resource competition were much weaker in the phyllosphere when compared to in vitro experiments. When investigating growth dynamics and reproductive success at the single-cell resolution, resource overlap and phylogenetic relationships are only weakly correlated with epiphytic Pe299R reproductive success, indicating that the leaf's spatial heterogeneity mitigates resource competition. Although the correlation is weak, the presence of competitors led to the development of Pe299R subpopulations that experienced different life histories and cell divisions. In some in planta competitions, Pe299R benefitted from the presence of epiphytes despite high resource overlap to the competitor strain suggesting other factors having stronger effects than resource competition. This study provides fundamental insights into how bacterial communities are shaped in heterogeneous environments and a framework to predict competition outcomes.
Collapse
Affiliation(s)
- Rudolf O Schlechter
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand.
- Bioprotection Research Core, University of Canterbury, Christchurch, 8011, New Zealand.
| | - Evan J Kear
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Michał Bernach
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8011, New Zealand
| | - Daniela M Remus
- Protein Science and Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N P Remus-Emsermann
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand.
- Bioprotection Research Core, University of Canterbury, Christchurch, 8011, New Zealand.
| |
Collapse
|
7
|
Weiss AS, Niedermeier LS, von Strempel A, Burrichter AG, Ring D, Meng C, Kleigrewe K, Lincetto C, Hübner J, Stecher B. Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community. Nat Commun 2023; 14:4780. [PMID: 37553336 PMCID: PMC10409746 DOI: 10.1038/s41467-023-40372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/24/2023] [Indexed: 08/10/2023] Open
Abstract
A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.
Collapse
Affiliation(s)
- Anna S Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Lisa S Niedermeier
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna G Burrichter
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Chiara Lincetto
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Johannes Hübner
- Division of Paediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany.
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany.
| |
Collapse
|
8
|
Martins SJ, Pasche J, Silva HAO, Selten G, Savastano N, Abreu LM, Bais HP, Garrett KA, Kraisitudomsook N, Pieterse CMJ, Cernava T. The Use of Synthetic Microbial Communities to Improve Plant Health. PHYTOPATHOLOGY 2023; 113:1369-1379. [PMID: 36858028 DOI: 10.1094/phyto-01-23-0016-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.
Collapse
Affiliation(s)
- Samuel J Martins
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Josephine Pasche
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Hiago Antonio O Silva
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Gijs Selten
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Noah Savastano
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Lucas Magalhães Abreu
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Karen A Garrett
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | | | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8020, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
| |
Collapse
|
9
|
Li L, Liu Y, Xiao Q, Xiao Z, Meng D, Yang Z, Deng W, Yin H, Liu Z. Dissecting the HGT network of carbon metabolic genes in soil-borne microbiota. Front Microbiol 2023; 14:1173748. [PMID: 37485539 PMCID: PMC10361621 DOI: 10.3389/fmicb.2023.1173748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/25/2023] Open
Abstract
The microbiota inhabiting soil plays a significant role in essential life-supporting element cycles. Here, we investigated the occurrence of horizontal gene transfer (HGT) and established the HGT network of carbon metabolic genes in 764 soil-borne microbiota genomes. Our study sheds light on the crucial role of HGT components in microbiological diversification that could have far-reaching implications in understanding how these microbial communities adapt to changing environments, ultimately impacting agricultural practices. In the overall HGT network of carbon metabolic genes in soil-borne microbiota, a total of 6,770 nodes and 3,812 edges are present. Among these nodes, phyla Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes are predominant. Regarding specific classes, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, Actinomycetia, Betaproteobacteria, and Clostridia are dominant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional assignments of glycosyltransferase (18.5%), glycolysis/gluconeogenesis (8.8%), carbohydrate-related transporter (7.9%), fatty acid biosynthesis (6.5%), benzoate degradation (3.1%) and butanoate metabolism (3.0%) are primarily identified. Glycosyltransferase involved in cell wall biosynthesis, glycosylation, and primary/secondary metabolism (with 363 HGT entries), ranks first overwhelmingly in the list of most frequently identified carbon metabolic HGT enzymes, followed by pimeloyl-ACP methyl ester carboxylesterase, alcohol dehydrogenase, and 3-oxoacyl-ACP reductase. Such HGT events mainly occur in the peripheral functions of the carbon metabolic pathway instead of the core section. The inter-microbe HGT genetic traits in soil-borne microbiota genetic sequences that we recognized, as well as their involvement in the metabolism and regulation processes of carbon organic, suggest a pervasive and substantial effect of HGT on the evolution of microbes.
Collapse
Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Qinzhi Xiao
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Zhipeng Xiao
- Hengyang Tobacco Company of Hunan Province, Hengyang, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Wenqiao Deng
- Changsha Institute of Agricultural Science, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| |
Collapse
|
10
|
Gutierrez-Vilchis A, Perfecto-Avalos Y, Garcia-Gonzalez A. Modeling bacteria pairwise interactions in human microbiota by Sparse Identification of Nonlinear Dynamics (SINDy) . ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083503 DOI: 10.1109/embc40787.2023.10341078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The gut microbiota is a community of high complexity; its composition changes due to ecological interactions, these are studied to understand the relationship with the human health. External stimuli like the administration of probiotics, prebiotics, or drugs are known to modify these interactions. The high complexity of microbiota composition can be studied by considering pairwise interactions. Pairwise interactions in bacterial communities consider each species' directionality and impact on one another, e.g., commensalism (unidirectional positive interaction) or competition (bidirectional negative interaction). These interactions can either be interspecies or intraspecies. The Lotka-Volterra (LV) model has been implemented to characterize these bacteria interactions, considering the ecological relationship among the different species presented. One of the main challenges is determining the specific interaction parameters in LV structure from experimental data. This study implemented a novel approach based on the sparse identification of nonlinear dynamic method (SINDy). One of the assumptions in SINDy method implies the knowledge of the data derivative structure. To fulfill this requirement, a differential neural network algorithm was implemented. We assessed the performance of this approach considering both a simulated and experimental interspecies scenario. A two-species bacterial LV model was simulated in the initial validation stage, and the resulting kinetic growth data was recorded. This data was utilized for training a differential neural network algorithm, which was used to derive a time-derivative structure for the dataset. After this step, SINDy method was implemented to calculate the interaction parameters. Three conditions were evaluated in intraspecies competition, obtaining an average identification parametric error of less than 2%. For experimental data, parametric analysis results are sensitive to detect the influence of a drug presence over the intraspecies interaction with a reduction of 50% in its typical values.Clinical Relevance- In this study, we devised a strategy to determine how two species of the human gastrointestinal microbiota interact and the impact of drug administration on these interactions.
Collapse
|
11
|
Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome. MICROBIOME 2022; 10:217. [PMID: 36482420 PMCID: PMC9733318 DOI: 10.1186/s40168-022-01383-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 09/23/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND From a theoretical ecology point of view, microbiomes are far more complex than expected. Besides competition and competitive exclusion, cooperative microbe-microbe interactions have to be carefully considered. Metabolic dependencies among microbes likely explain co-existence in microbiota. METHODOLOGY In this in silico study, we explored genome-scale metabolic models (GEMs) of 193 bacteria isolated from Arabidopsis thaliana roots. We analyzed their predicted producible metabolites under simulated nutritional constraints including "root exudate-mimicking growth media" and assessed the potential of putative metabolic exchanges of by- and end-products to avoid those constraints. RESULTS We found that the genome-encoded metabolic potential is quantitatively and qualitatively clustered by phylogeny, highlighting metabolic differentiation between taxonomic groups. Random, synthetic combinations of increasing numbers of strains (SynComs) indicated that the number of producible compounds by GEMs increased with average phylogenetic distance, but that most SynComs were centered around an optimal phylogenetic distance. Moreover, relatively small SynComs could reflect the capacity of the whole community due to metabolic redundancy. Inspection of 30 specific end-product metabolites (i.e., target metabolites: amino acids, vitamins, phytohormones) indicated that the majority of the strains had the genetic potential to produce almost all the targeted compounds. Their production was predicted (1) to depend on external nutritional constraints and (2) to be facilitated by nutritional constraints mimicking root exudates, suggesting nutrient availability and root exudates play a key role in determining the number of producible metabolites. An answer set programming solver enabled the identification of numerous combinations of strains predicted to depend on each other to produce these targeted compounds under severe nutritional constraints thus indicating a putative sub-community level of functional redundancy. CONCLUSIONS This study predicts metabolic restrictions caused by available nutrients in the environment. By extension, it highlights the importance of the environment for niche potential, realization, partitioning, and overlap. Our results also suggest that metabolic dependencies and cooperation among root microbiota members compensate for environmental constraints and help maintain co-existence in complex microbial communities. Video Abstract.
Collapse
Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Campus Beaulieu, 35000, Rennes, France
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | - Nathan Vannier
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany
| | | | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, 50829, Cologne, Germany.
| |
Collapse
|
12
|
Ollison GA, Hu SK, Hopper JV, Stewart BP, Smith J, Beatty JL, Rink LK, Caron DA. Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight). Environ Microbiol 2022; 24:6033-6051. [PMID: 35880671 PMCID: PMC10087728 DOI: 10.1111/1462-2920.16137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/12/2023]
Abstract
Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2 . Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes in relative abundance dynamics of the metabolically active protistan community were followed via expressed 18S V4 rRNA genes (RNA) throughout two algal blooms during the spring of 2018 and 2019 in Santa Monica Bay (central Southern California Bight). A diatom bloom formed after wind-driven, nutrient upwelling events in both years, but different taxa dominated each year. Whereas diatoms bloomed following elevated nutrients and declined after depletion each year, a massive dinoflagellate bloom manifested under relatively low inorganic nitrogen conditions following diatom bloom senescence in 2019 but not 2018. Network analysis revealed associations between diatoms and cercozoan putative parasitic taxa and syndinean parasites during 2019 that may have influenced the demise of the diatoms, and the transition to a dinoflagellate-dominated bloom.
Collapse
Affiliation(s)
- Gerid A Ollison
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Sarah K Hu
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, Massachusetts, USA
| | - Julie V Hopper
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Brittany P Stewart
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jayme Smith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jennifer L Beatty
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Laura K Rink
- Heal the Bay Aquarium, Santa Monica, California, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| |
Collapse
|
13
|
Classifying Interactions in a Synthetic Bacterial Community Is Hindered by Inhibitory Growth Medium. mSystems 2022; 7:e0023922. [PMID: 36197097 PMCID: PMC9600862 DOI: 10.1128/msystems.00239-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Predicting the fate of a microbial community and its member species relies on understanding the nature of their interactions. However, designing simple assays that distinguish between interaction types can be challenging. Here, we performed spent medium assays based on the predictions of a mathematical model to decipher the interactions among four bacterial species: Agrobacterium tumefaciens, Comamonas testosteroni, Microbacterium saperdae, and Ochrobactrum anthropi. While most experimental results matched model predictions, the behavior of C. testosteroni did not: its lag phase was reduced in the pure spent media of A. tumefaciens and M. saperdae but prolonged again when we replenished our growth medium. Further experiments showed that the growth medium actually delayed the growth of C. testosteroni, leading us to suspect that A. tumefaciens and M. saperdae could alleviate this inhibitory effect. There was, however, no evidence supporting such "cross-detoxification," and instead, we identified metabolites secreted by A. tumefaciens and M. saperdae that were then consumed or "cross-fed" by C. testosteroni, shortening its lag phase. Our results highlight that even simple, defined growth media can have inhibitory effects on some species and that such negative effects need to be included in our models. Based on this, we present new guidelines to correctly distinguish between different interaction types such as cross-detoxification and cross-feeding. IMPORTANCE Communities of microbes colonize virtually every place on earth. Ultimately, we strive to predict and control how these communities behave, for example, if they reside in our guts and make us sick. But precise control is impossible unless we can identify exactly how their member species interact with one another. To find a systematic way to measure interactions, we started very simply with a small community of four bacterial species and carefully designed experiments based on a mathematical model. This first attempt accurately mapped out interactions for all species except one. By digging deeper, we understood that our method failed for that species as it was suffering in the growth medium that we chose. A revised model that considered that growth media can be harmful could then make more accurate predictions. What we have learned with these four species can now be applied to decipher interactions in larger communities.
Collapse
|
14
|
Chaudhuri S, Srivastava A. Network approach to understand biological systems: From single to multilayer networks. J Biosci 2022. [DOI: 10.1007/s12038-022-00285-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Biofilm through the Looking Glass: A Microbial Food Safety Perspective. Pathogens 2022; 11:pathogens11030346. [PMID: 35335670 PMCID: PMC8954374 DOI: 10.3390/pathogens11030346] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Food-processing facilities harbor a wide diversity of microorganisms that persist and interact in multispecies biofilms, which could provide an ecological niche for pathogens to better colonize and gain tolerance against sanitization. Biofilm formation by foodborne pathogens is a serious threat to food safety and public health. Biofilms are formed in an environment through synergistic interactions within the microbial community through mutual adaptive response to their long-term coexistence. Mixed-species biofilms are more tolerant to sanitizers than single-species biofilms or their planktonic equivalents. Hence, there is a need to explore how multispecies biofilms help in protecting the foodborne pathogen from common sanitizers and disseminate biofilm cells from hotspots and contaminate food products. This knowledge will help in designing microbial interventions to mitigate foodborne pathogens in the processing environment. As the global need for safe, high-quality, and nutritious food increases, it is vital to study foodborne pathogen behavior and engineer new interventions that safeguard food from contamination with pathogens. This review focuses on the potential food safety issues associated with biofilms in the food-processing environment.
Collapse
|
16
|
Pretorius IS. Visualising the next frontiers in wine yeast research. FEMS Yeast Res 2022; 22:6530195. [PMID: 35175339 PMCID: PMC8916113 DOI: 10.1093/femsyr/foac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
A range of game-changing biodigital and biodesign technologies are coming of age all around us, transforming our world in complex ways that are hard to predict. Not a day goes by without news of how data-centric engineering, algorithm-driven modelling, and biocyber technologies—including the convergence of artificial intelligence, machine learning, automated robotics, quantum computing, and genome editing—will change our world. If we are to be better at expecting the unexpected in the world of wine, we need to gain deeper insights into the potential and limitations of these technological developments and advances along with their promise and perils. This article anticipates how these fast-expanding bioinformational and biodesign toolkits might lead to the creation of synthetic organisms and model systems, and ultimately new understandings of biological complexities could be achieved. A total of four future frontiers in wine yeast research are discussed in this article: the construction of fully synthetic yeast genomes, including minimal genomes; supernumerary pan-genome neochromosomes; synthetic metagenomes; and synthetic yeast communities. These four concepts are at varying stages of development with plenty of technological pitfalls to overcome before such model chromosomes, genomes, strains, and yeast communities could illuminate some of the ill-understood aspects of yeast resilience, fermentation performance, flavour biosynthesis, and ecological interactions in vineyard and winery settings. From a winemaker's perspective, some of these ideas might be considered as far-fetched and, as such, tempting to ignore. However, synthetic biologists know that by exploring these futuristic concepts in the laboratory could well forge new research frontiers to deepen our understanding of the complexities of consistently producing fine wines with different fermentation processes from distinctive viticultural terroirs. As the saying goes in the disruptive technology industry, it take years to create an overnight success. The purpose of this article is neither to glorify any of these concepts as a panacea to all ills nor to crucify them as a danger to winemaking traditions. Rather, this article suggests that these proposed research endeavours deserve due consideration because they are likely to cast new light on the genetic blind spots of wine yeasts, and how they interact as communities in vineyards and wineries. Future-focussed research is, of course, designed to be subject to revision as new data and technologies become available. Successful dislodging of old paradigms with transformative innovations will require open-mindedness and pragmatism, not dogmatism—and this can make for a catch-22 situation in an archetypal traditional industry, such as the wine industry, with its rich territorial and socio-cultural connotations.
Collapse
Affiliation(s)
- I S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
17
|
Jenior ML, Papin JA. Computational approaches to understanding Clostridioides difficile metabolism and virulence. Curr Opin Microbiol 2022; 65:108-115. [PMID: 34839237 PMCID: PMC8792252 DOI: 10.1016/j.mib.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The progress of infection by Clostridioides difficile is strongly influenced by metabolic cues it encounters as it colonizes the gastrointestinal tract. Both colonization and regulation of virulence have a multi-factorial interaction between host, microbiome, and gene expression cascades. While these connections with metabolism have been understood for some time, many mechanisms of control have remained difficult to directly assay due to high metabolic variability among C. difficile isolates and difficult genetic systems. Computational systems offer a means to interrogate structure of complex or noisy datasets and generate useful, tractable hypotheses to be tested in the laboratory. Recently, in silico techniques have provided powerful insights into metabolic elements of C. difficile infection ranging from virulence regulation to interactions with the gut microbiota. In this review, we introduce and provide context to the methods of computational modeling that have been applied to C. difficile metabolism and virulence thus far. The techniques discussed here have laid the foundation for future multi-scale efforts aimed at understanding the complex interplay of metabolic activity between pathogen, host, and surrounding microbial community in the regulation of C. difficile pathogenesis.
Collapse
Affiliation(s)
- Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
| |
Collapse
|
18
|
Mataigne V, Vannier N, Vandenkoornhuyse P, Hacquard S. Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes. Front Microbiol 2022; 12:780469. [PMID: 34987488 PMCID: PMC8721230 DOI: 10.3389/fmicb.2021.780469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/25/2021] [Indexed: 12/26/2022] Open
Abstract
Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
Collapse
Affiliation(s)
- Victor Mataigne
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nathan Vannier
- Université de Rennes 1, CNRS, UMR6553 ECOBIO, Rennes, France
| | | | | |
Collapse
|
19
|
Ábrego-Gacía A, Poggi-Varaldo HM, Robles-González V, Ponce-Noyola T, Calva-Calva G, Ríos-Leal E, Estrada-Bárcenas D, Mendoza-Vargas A. Lovastatin as a supplement to mitigate rumen methanogenesis: an overview. J Anim Sci Biotechnol 2021; 12:123. [PMID: 34911584 PMCID: PMC8675506 DOI: 10.1186/s40104-021-00641-8] [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: 05/30/2021] [Accepted: 10/03/2021] [Indexed: 11/23/2022] Open
Abstract
Methane from enteric fermentation is the gas with the greatest environmental impact emitted by ruminants. Lovastatin (Lv) addition to feedstocks could be a strategy to mitigate rumen methane emissions via decreasing the population of methanogenic archaea (MA). Thus, this paper provides the first overview of the effects of Lv supplementation, focusing on the inhibition of methane production, rumen microbiota, and ruminal fermentation. Results indicated that Lv treatment had a strong anti-methanogenic effect on pure strains of MA. However, there are uncertainties from in vitro rumen fermentation trials with complex substrates and rumen inoculum. Solid-state fermentation (SSF) has emerged as a cost-effective option to produce Lv. In this way, SSF of agricultural residues as an Lv-carrier supplement in sheep and goats demonstrated a consistent decrease in ruminal methane emissions. The experimental evidence for in vitro conditions showed that Lv did not affect the volatile fatty acids (VFA). However, in vivo experiments demonstrated that the production of VFA was decreased. Lv did not negatively affect the digestibility of dry matter during in vitro and in vivo methods, and there is even evidence that it can induce an increase in digestibility. Regarding the rumen microbiota, populations of MA were reduced, and no differences were detected in alpha and beta diversity associated with Lv treatment. However, some changes in the relative abundance of the microbiota were induced. Further studies are recommended on: (i) Lv biodegradation products and stability, as well as its adsorption onto the solid matter in the rumen, to gain more insight on the “available” or effective Lv concentration; and (ii) to determine whether the effect of Lv on ruminal fermentation also depends on the feed composition and different ruminants.
Collapse
Affiliation(s)
- Amaury Ábrego-Gacía
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Héctor M Poggi-Varaldo
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico. .,Environmental Biotechnology and Renewable Energies Group, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico.
| | - Vania Robles-González
- Instituto de Hidrología, Universidad Tecnológica de la Mixteca, Oaxaca, 69000, Huajuapan de León, Mexico
| | - Teresa Ponce-Noyola
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Graciano Calva-Calva
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Elvira Ríos-Leal
- Department of Biotechnology and Bioengineering, CINVESTAV-IPN, P.O.Box 17-740, 07000, Mexico City, Mexico
| | - Daniel Estrada-Bárcenas
- National Collection of Microbial and Cellular Cultures, CINVESTAV-IPN, P.O.Box17-740, 07000, Mexico City, Mexico
| | - Alfredo Mendoza-Vargas
- Unidad de Secuenciación e Identificación de Polimorfismos, Instituto Nacional de Medicina Genómica, 14610, Mexico City, Mexico
| |
Collapse
|
20
|
Dong C, Shao Q, Zhang Q, Yao T, Huang J, Liang Z, Han Y. Preferences for core microbiome composition and function by different definition methods: Evidence for the core microbiome of Eucommia ulmoides bark. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148091. [PMID: 34380268 DOI: 10.1016/j.scitotenv.2021.148091] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
The core microbiome, as a unique group of microorganisms, is an emerging research hotspot that provides a new opportunity to improve growth and production of a host. However, the subjectivity associated with the concept of "core microbiome" means there is currently no uniform definition method for the core microbiome. In this study, the strengths and limitations of four commonly used definition methods for the core microbiome were explored from composition to function based on the 16S rRNA gene dataset of Eucommia ulmoides bark from 25 different biogeographical regions in China. There were differences in the composition of the core microbiomes defined by the different methods. The four definition methods of phylogeny, membership, composition, and network connection contained 274, 10, 5, and 5 core OTUs (operational taxonomic units), respectively. In contrast, the core microbiomes defined by different methods displayed similarities in function. In addition, different definition methods showed varying preferences for abundant taxa, intermediate taxa, and rare taxa. Some core taxa defined by the definition method of phylogeny were significantly associated with pharmacologically active ingredients of E. ulmoides bark. The findings of this study suggest that although the core microbiomes defined by different methods have preferences in composition and function, the term refers to a group of microbes that are particularly notable and important for host-associated microbiomes. Therefore, we propose: (I) The definition method of the core microbiome should be selected according to the ecological problems faced; (II) A combination of multiple methods may comprehensively reveal the core microbiome at different levels of the host, and may also facilitate understanding of the ecological and evolutionary processes that govern host-microbe interactions.
Collapse
Affiliation(s)
- Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Qingqing Zhang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan 245041, Anhui, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350108, Fujian, China
| | - Zongqi Liang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, Guizhou, China.
| |
Collapse
|
21
|
Martínez Arbas S, Busi SB, Queirós P, de Nies L, Herold M, May P, Wilmes P, Muller EEL, Narayanasamy S. Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies. Front Genet 2021; 12:666244. [PMID: 34194470 PMCID: PMC8236828 DOI: 10.3389/fgene.2021.666244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, multi-omic studies have enabled resolving community structure and interrogating community function of microbial communities. Simultaneous generation of metagenomic, metatranscriptomic, metaproteomic, and (meta) metabolomic data is more feasible than ever before, thus enabling in-depth assessment of community structure, function, and phenotype, thus resulting in a multitude of multi-omic microbiome datasets and the development of innovative methods to integrate and interrogate those multi-omic datasets. Specifically, the application of reference-independent approaches provides opportunities in identifying novel organisms and functions. At present, most of these large-scale multi-omic datasets stem from spatial sampling (e.g., water/soil microbiomes at several depths, microbiomes in/on different parts of the human anatomy) or case-control studies (e.g., cohorts of human microbiomes). We believe that longitudinal multi-omic microbiome datasets are the logical next step in microbiome studies due to their characteristic advantages in providing a better understanding of community dynamics, including: observation of trends, inference of causality, and ultimately, prediction of community behavior. Furthermore, the acquisition of complementary host-derived omics, environmental measurements, and suitable metadata will further enhance the aforementioned advantages of longitudinal data, which will serve as the basis to resolve drivers of community structure and function to understand the biotic and abiotic factors governing communities and specific populations. Carefully setup future experiments hold great potential to further unveil ecological mechanisms to evolution, microbe-microbe interactions, or microbe-host interactions. In this article, we discuss the challenges, emerging strategies, and best-practices applicable to longitudinal microbiome studies ranging from sampling, biomolecular extraction, systematic multi-omic measurements, reference-independent data integration, modeling, and validation.
Collapse
Affiliation(s)
- Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pedro Queirós
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Malte Herold
- Department of Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emilie E. L. Muller
- Université de Strasbourg, UMR 7156 CNRS, Génétique Moléculaire, Génomique, Microbiologie, Strasbourg, France
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| |
Collapse
|
22
|
Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, Dittami SM. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 2021; 9:e11344. [PMID: 33996285 PMCID: PMC8106915 DOI: 10.7717/peerj.11344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/03/2021] [Indexed: 01/29/2023] Open
Abstract
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
Collapse
Affiliation(s)
- Elham Karimi
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Enora Geslain
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France.,FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Arnaud Belcour
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Méziane Aïte
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Anne Siegel
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Erwan Corre
- FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Simon M Dittami
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| |
Collapse
|
23
|
Belda I, Williams TC, de Celis M, Paulsen IT, Pretorius IS. Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell. Nat Commun 2021; 12:1599. [PMID: 33707418 PMCID: PMC7952416 DOI: 10.1038/s41467-021-21877-y] [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] [Received: 12/21/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
Collapse
Affiliation(s)
- Ignacio Belda
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Thomas C. Williams
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Miguel de Celis
- grid.4795.f0000 0001 2157 7667Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Ian T. Paulsen
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Isak S. Pretorius
- grid.1004.50000 0001 2158 5405Department of Molecular Sciences, and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| |
Collapse
|
24
|
Mabwi HA, Kim E, Song DG, Yoon HS, Pan CH, Komba E, Ko G, Cha KH. Synthetic gut microbiome: Advances and challenges. Comput Struct Biotechnol J 2020; 19:363-371. [PMID: 33489006 PMCID: PMC7787941 DOI: 10.1016/j.csbj.2020.12.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
An exponential rise in studies regarding the association among human gut microbial communities, human health, and diseases is currently attracting the attention of researchers to focus on human gut microbiome research. However, even with the ever-growing number of studies on the human gut microbiome, translation into improved health is progressing slowly. This hampering is due to the complexities of the human gut microbiome, which is composed of >1,000 species of microorganisms, such as bacteria, archaea, viruses, and fungi. To overcome this complexity, it is necessary to reduce the gut microbiome, which can help simplify experimental variables to an extent, such that they can be deliberately manipulated and controlled. Reconstruction of synthetic or established gut microbial communities would make it easier to understand the structure, stability, and functional activities of the complex microbial community of the human gut. Here, we provide an overview of the developments and challenges of the synthetic human gut microbiome, and propose the incorporation of multi-omics and mathematical methods in a better synthetic gut ecosystem design, for easy translation of microbiome information to therapies.
Collapse
Affiliation(s)
- Humphrey A. Mabwi
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 25523, Tanzania
| | - Eunjung Kim
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Dae-Geun Song
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Hyo Shin Yoon
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Cheol-Ho Pan
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| | - Erick.V.G. Komba
- SACIDS Foundation for One Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro 25523, Tanzania
| | - GwangPyo Ko
- Department of Environmental Health Sciences, School of Public Health, Seoul National University, Seoul 08826, Republic of Korea
- Center for Human and Environmental Microbiome, Seoul National University, Seoul 08826, Republic of Korea
- KoBioLabs, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kwang Hyun Cha
- KIST Gangneung Institute of Natural Products, Gangneung 25451, Republic of Korea
| |
Collapse
|
25
|
Altamirano Á, Saa PA, Garrido D. Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools. Comput Struct Biotechnol J 2020; 18:3897-3904. [PMID: 33335687 PMCID: PMC7719866 DOI: 10.1016/j.csbj.2020.11.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 02/07/2023] Open
Abstract
The human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been great progress in the field driven by metagenomics and experimental studies, the mechanisms underpinning microbial composition and interactions in the microbiome remain poorly understood. Genome-scale metabolic models are mathematical structures capable of describing the metabolic potential of microbial cells. They are thus suitable tools for probing the metabolic properties of microbial communities. In this review, we discuss the most recent and relevant genome-scale metabolic modelling tools for inferring the composition, interactions, and ultimately, biological function of the constituent species of a microbial community with special emphasis in the gut microbiota. Particular attention is given to constraint-based metabolic modelling methods as well as hybrid agent-based methods for capturing the interactions and behavior of the community in time and space. Finally, we discuss the challenges hindering comprehensive modelling of complex microbial communities and its application for the in-silico design of microbial consortia with therapeutic functions.
Collapse
|
26
|
Greslehner GP. Not by structures alone: Can the immune system recognize microbial functions? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2020; 84:101336. [PMID: 32830048 DOI: 10.1016/j.shpsc.2020.101336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
A central question for immunology is: what does the immune system recognize and according to which principles does this kind of recognition work? Immunology has been dominated by the idea of recognizing molecular structures and triggering an appropriate immune response when facing non-self or danger. Recently, characterizations in terms of function have turned out to be more conserved and explanatory in microbiota research than taxonomic composition for understanding microbiota-host interactions. Starting from a conceptual analysis of the notions of structure and function, I raise the title question whether it is possible for the immune system to recognize microbial functions. I argue that this is indeed the case, making the claim that some function-associated molecular patterns are not indicative of the presence of certain taxa (''who is there'') but of biochemical activities and effects (''what is going on''). In addition, I discuss case studies which show that there are immunological sensors that can directly detect microbial activities, irrespective of their specific structural manifestation. At the same time, the discussed account puts the causal role notions of function on a more realist and objective basis.
Collapse
Affiliation(s)
- Gregor P Greslehner
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, 33076, Bordeaux, France.
| |
Collapse
|
27
|
|
28
|
The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae. ISME JOURNAL 2020; 15:746-761. [PMID: 33093620 DOI: 10.1038/s41396-020-00810-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Microbial communities are comprised of many species that coexist on small spatial scales. This is difficult to explain because many interspecies interactions are competitive, and ecological theory predicts that one species will drive the extinction of another species that competes for the same resource. Conversely, evolutionary theory proposes that natural selection can lead to coexistence by driving competing species to use non-overlapping resources. However, evolutionary escape from extinction may be slow compared to the rate of competitive exclusion. Here, we use experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae to study the evolution of coexistence in species that compete for resources. We find that while E. coli usually outcompetes S. cerevisiae in co-culture, a few populations evolved stable coexistence after ~1000 generations of coevolution. We sequenced S. cerevisiae and E. coli populations, identified multi-hit genes, and engineered alleles from these genes into several genetic backgrounds, finding that some mutations modified interactions between E. coli and S. cerevisiae. Together, our data demonstrate that coexistence can evolve, de novo, from intense competition between two species with no history of coevolution.
Collapse
|
29
|
Herold M, Martínez Arbas S, Narayanasamy S, Sheik AR, Kleine-Borgmann LAK, Lebrun LA, Kunath BJ, Roume H, Bessarab I, Williams RBH, Gillece JD, Schupp JM, Keim PS, Jäger C, Hoopmann MR, Moritz RL, Ye Y, Li S, Tang H, Heintz-Buschart A, May P, Muller EEL, Laczny CC, Wilmes P. Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance. Nat Commun 2020; 11:5281. [PMID: 33077707 PMCID: PMC7572474 DOI: 10.1038/s41467-020-19006-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
The development of reliable, mixed-culture biotechnological processes hinges on understanding how microbial ecosystems respond to disturbances. Here we reveal extensive phenotypic plasticity and niche complementarity in oleaginous microbial populations from a biological wastewater treatment plant. We perform meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics) on in situ samples over 14 months at weekly intervals. Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct fundamental niche types. Throughout the time-series, we observe a major, transient shift in community structure, coinciding with substrate availability changes. Functional omics data reveals extensive variation in gene expression and substrate usage amongst community members. Ex situ bioreactor experiments confirm that responses occur within five hours of a pulse disturbance, demonstrating rapid adaptation by specific populations. Our results show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity, and set the foundation for future ecological engineering efforts. Herold et al. present an integrated meta-omics framework to investigate how mixed microbial communities, such as oleaginous bacterial populations in biological wastewater treatment plants, respond with distinct adaptation strategies to disturbances. They show that community resistance and resilience are a function of phenotypic plasticity and niche complementarity.
Collapse
Affiliation(s)
- Malte Herold
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Epidemiology and Microbial Genomics, Laboratoire National de Santé, 1 rue Louis Rech, 3555, Dudelange, Luxembourg
| | - Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Megeno S.A., 6A Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Abdul R Sheik
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Luise A K Kleine-Borgmann
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Laura A Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Benoît J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Hugo Roume
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,MetaGenoPolis, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université Paris-Saclay, Domaine de Vilvert, Bâtiment 325, 78350, Jouy-en-Josas, France
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Dr, Singapore, 637551, Singapore
| | - John D Gillece
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - James M Schupp
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - Paul S Keim
- The Translational Genomics Research Institute, 3051 West Shamrell Boulevard, Flagstaff, AZ, 86001, USA
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Yuzhen Ye
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Sujun Li
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Haixu Tang
- School of Informatics, Computing and Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, IN, 47405, USA
| | - Anna Heintz-Buschart
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, 04103, Leipzig, Germany.,Helmholtz Centre for Environmental Research GmbH - UFZ, Theodor-Lieser-Str. 4, 06120, Halle, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Emilie E L Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg.,Equipe Adaptations et Interactions Microbiennes, UMR 7156 UNISTRA-CNRS, Université de Strasbourg, Strasbourg, France
| | - Cedric C Laczny
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg, Luxembourg. .,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
30
|
Marinos G, Kaleta C, Waschina S. Defining the nutritional input for genome-scale metabolic models: A roadmap. PLoS One 2020; 15:e0236890. [PMID: 32797084 PMCID: PMC7428157 DOI: 10.1371/journal.pone.0236890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/15/2020] [Indexed: 12/13/2022] Open
Abstract
The reconstruction and application of genome-scale metabolic network models is a central topic in the field of systems biology with numerous applications in biotechnology, ecology, and medicine. However, there is no agreed upon standard for the definition of the nutritional environment for these models. The objective of this article is to provide a guideline and a clear paradigm on how to translate nutritional information into an in-silico representation of the chemical environment. Step-by-step procedures explain how to characterise and categorise the nutritional input and to successfully apply it to constraint-based metabolic models. In parallel, we illustrate the proposed procedure with a case study of the growth of Escherichia coli in a complex nutritional medium and show that an accurate representation of the medium is crucial for physiological predictions. The proposed framework will assist researchers to expand their existing metabolic models of their microbial systems of interest with detailed representations of the nutritional environment, which allows more accurate and reproducible predictions of microbial metabolic processes.
Collapse
Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Division of Nutriinformatics, Institute for Human Nutrition and Food Sciences, Kiel University, Kiel, Schleswig-Holstein, Germany
| |
Collapse
|
31
|
Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol 2020; 18:607-621. [DOI: 10.1038/s41579-020-0412-1] [Citation(s) in RCA: 597] [Impact Index Per Article: 149.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2020] [Indexed: 01/17/2023]
|
32
|
Chan JY, Bonser SP, Powell JR, Cornwell WK. Environmental cues for dispersal in a filamentous fungus in simulated islands. OIKOS 2020. [DOI: 10.1111/oik.07000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin Y. Chan
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, Univ. of New South Wales Sydney New South Wales 2052 Australia
| | - Stephen P. Bonser
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, Univ. of New South Wales Sydney New South Wales 2052 Australia
| | - Jeff R. Powell
- Hawkesbury Inst. for the Environment, Western Sydney Univ. Penrith NSW Australia
| | - William K. Cornwell
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, Univ. of New South Wales Sydney New South Wales 2052 Australia
| |
Collapse
|
33
|
Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host-microbial interactions. Biochem Soc Trans 2020; 48:901-913. [PMID: 32379295 DOI: 10.1042/bst20190667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 01/24/2023]
Abstract
Systems modelled in the context of molecular and cellular biology are difficult to represent with a single calibrated numerical model. Flux optimisation hypotheses have shown tremendous promise to accurately predict bacterial metabolism but they require a precise understanding of metabolic reactions occurring in the considered species. Unfortunately, this information may not be available for more complex organisms or non-cultured microorganisms such as those evidenced in microbiomes with metagenomic techniques. In both cases, flux optimisation techniques may not be applicable to elucidate systems functioning. In this context, we describe how automatic reasoning allows relevant features of an unconventional biological system to be identified despite a lack of data. A particular focus is put on the use of Answer Set Programming, a logic programming paradigm with combinatorial optimisation functionalities. We describe its usage to over-approximate metabolic responses of biological systems and solve gap-filling problems. In this review, we compare steady-states and Boolean abstractions of metabolic models and illustrate their complementarity via applications to the metabolic analysis of macro-algae. Ongoing applications of this formalism explore the emerging field of systems ecology, notably elucidating interactions between a consortium of microbes and a host organism. As the first step in this field, we will illustrate how the reduction in microbiotas according to expected metabolic phenotypes can be addressed with gap-filling problems.
Collapse
|
34
|
Tal O, Selvaraj G, Medina S, Ofaim S, Freilich S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020; 8:microorganisms8060840. [PMID: 32503277 PMCID: PMC7356744 DOI: 10.3390/microorganisms8060840] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and different combinations of microorganisms. NetMet is a web-based tool and a software package for predicting the metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes, as input, lists of (i) species-specific enzymatic reactions (EC numbers), and (ii) relevant metabolic environments. The algorithm generates, as output, lists of (i) compounds that individual species can produce in each given environment, and (ii) compounds that are predicted to be produced through complementary interactions. The tool is demonstrated in two case studies. First, we compared the metabolic capacities of different haplotypes of the obligatory fruit and vegetable pathogen Candidatus Liberibacter solanacearum to those of their culturable taxonomic relative Liberibacter crescens. Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly Bemisia tabaci.
Collapse
|
35
|
Greslehner GP. Microbiome Structure and Function: A New Framework for Interpreting Data. Bioessays 2020; 42:e1900255. [DOI: 10.1002/bies.201900255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Gregor P. Greslehner
- University of Bordeaux and CNRS – ImmunoConcept UMR5164, 146 rue Léo Saignat Bordeaux 33076 France
| |
Collapse
|
36
|
Abstract
This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data. High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With metatranscriptomics, it is possible to interrogate the transcriptomes of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic data sets contain a rich suite of additional information that is just beginning to be explored. Here, we focus on antisense expression in metatranscriptomics, discuss the different computational strategies for handling it, and highlight the strengths but also potentially detrimental effects on downstream analysis and interpretation. We also analyzed the antisense transcriptomes of multiple genomes and metagenome-assembled genomes (MAGs) from five different data sets and found high variability in the levels of antisense transcription for individual species, which were consistent across samples. Importantly, we challenged the conceptual framework that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from the combined effect of unknown biological and technical factors. Antisense transcription can be highly informative, including technical details about data quality and novel insight into the biology of complex microbial communities. IMPORTANCE This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our understanding of antisense expression as well as interpretation of metatranscriptomic data in general. This analysis highlights that in some environments, antisense expression from microbial communities can dominate over regular gene expression. We explored some potential drivers of antisense transcription, but more importantly, this study serves as a starting point, highlighting topics for future research and providing guidelines to include antisense expression in generic bioinformatic pipelines for metatranscriptomic data.
Collapse
|
37
|
Baffy G. Gut Microbiota and Cancer of the Host: Colliding Interests. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1219:93-107. [PMID: 32130695 DOI: 10.1007/978-3-030-34025-4_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cancer develops in multicellular organisms from cells that ignore the rules of cooperation and escape the mechanisms of anti-cancer surveillance. Tumorigenesis is jointly encountered by the host and microbiota, a vast collection of microorganisms that live on the external and internal epithelial surfaces of the body. The largest community of human microbiota resides in the gastrointestinal tract where commensal, symbiotic and pathogenic microorganisms interact with the intestinal barrier and gut mucosal lymphoid tissue, creating a tumor microenvironment in which cancer cells thrive or perish. Aberrant composition and function of the gut microbiota (dysbiosis) has been associated with tumorigenesis by inducing inflammation, promoting cell growth and proliferation, weakening immunosurveillance, and altering food and drug metabolism or other biochemical functions of the host. However, recent research has also identified several mechanisms through which gut microbiota support the host in the fight against cancer. These mechanisms include the use of antigenic mimicry, biotransformation of chemotherapeutic agents, and other mechanisms to boost anti-cancer immune responses and improve the efficacy of cancer immunotherapy. Further research in this rapidly advancing field is expected to identify additional microbial metabolites with tumor suppressing properties, map the complex interactions of host-microbe 'transkingdom network' with cancer cells, and elucidate cellular and molecular pathways underlying the impact of specific intestinal microbial configurations on immune checkpoint inhibitor therapy.
Collapse
Affiliation(s)
- Gyorgy Baffy
- Department of Medicine, VA Boston Healthcare System and Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
38
|
Baquero F, Coque TM, Martínez JL, Aracil-Gisbert S, Lanza VF. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance. Front Microbiol 2019; 10:2892. [PMID: 31921068 PMCID: PMC6927996 DOI: 10.3389/fmicb.2019.02892] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.
Collapse
Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - José-Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sonia Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| |
Collapse
|
39
|
Wang T, Goyal A, Dubinkina V, Maslov S. Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comput Biol 2019; 15:e1007524. [PMID: 31856158 PMCID: PMC6922320 DOI: 10.1371/journal.pcbi.1007524] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/01/2019] [Indexed: 11/30/2022] Open
Abstract
The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of metabolic interactions between microbes, our model suggests about four trophic levels, each characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical metabolic environment of the gut (fecal metabolome) in approximate agreement with the real data. To understand the consequences of this trophic organization, we quantify the metabolic flow and biomass distribution, and explore patterns of microbial and metabolic diversity in different levels. The hierarchical trophic organization suggested by our model can help mechanistically establish causal links between the abundances of microbes and metabolites in the human gut.
Collapse
Affiliation(s)
- Tong Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Akshit Goyal
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Veronika Dubinkina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| |
Collapse
|
40
|
Vázquez-Castellanos JF, Biclot A, Vrancken G, Huys GRB, Raes J. Design of synthetic microbial consortia for gut microbiota modulation. Curr Opin Pharmacol 2019; 49:52-59. [DOI: 10.1016/j.coph.2019.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/12/2022]
|
41
|
Baltar F, Bayer B, Bednarsek N, Deppeler S, Escribano R, Gonzalez CE, Hansman RL, Mishra RK, Moran MA, Repeta DJ, Robinson C, Sintes E, Tamburini C, Valentin LE, Herndl GJ. Towards Integrating Evolution, Metabolism, and Climate Change Studies of Marine Ecosystems. Trends Ecol Evol 2019; 34:1022-1033. [DOI: 10.1016/j.tree.2019.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 11/30/2022]
|
42
|
McBain AJ, O'Neill CA, Amezquita A, Price LJ, Faust K, Tett A, Segata N, Swann JR, Smith AM, Murphy B, Hoptroff M, James G, Reddy Y, Dasgupta A, Ross T, Chapple IL, Wade WG, Fernandez-Piquer J. Consumer Safety Considerations of Skin and Oral Microbiome Perturbation. Clin Microbiol Rev 2019; 32:e00051-19. [PMID: 31366612 PMCID: PMC6750131 DOI: 10.1128/cmr.00051-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Microbiomes associated with human skin and the oral cavity are uniquely exposed to personal care regimes. Changes in the composition and activities of the microbial communities in these environments can be utilized to promote consumer health benefits, for example, by reducing the numbers, composition, or activities of microbes implicated in conditions such as acne, axillary odor, dandruff, and oral diseases. It is, however, important to ensure that innovative approaches for microbiome manipulation do not unsafely disrupt the microbiome or compromise health, and where major changes in the composition or activities of the microbiome may occur, these require evaluation to ensure that critical biological functions are unaffected. This article is based on a 2-day workshop held at SEAC Unilever, Sharnbrook, United Kingdom, involving 31 specialists in microbial risk assessment, skin and oral microbiome research, microbial ecology, bioinformatics, mathematical modeling, and immunology. The first day focused on understanding the potential implications of skin and oral microbiome perturbation, while approaches to characterize those perturbations were discussed during the second day. This article discusses the factors that the panel recommends be considered for personal care products that target the microbiomes of the skin and the oral cavity.
Collapse
Affiliation(s)
- Andrew J McBain
- Division of Pharmacy & Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
| | - Catherine A O'Neill
- Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, United Kingdom
| | - Alejandro Amezquita
- Unilever, Safety & Environmental Assurance Centre (SEAC), Sharnbrook, United Kingdom
| | - Laura J Price
- Unilever, Safety & Environmental Assurance Centre (SEAC), Sharnbrook, United Kingdom
| | - Karoline Faust
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Bacteriology, Rega Institute, Leuven, Belgium
| | - Adrian Tett
- Department CIBIO, University of Trento, Trento, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Jonathan R Swann
- Division of Integrative Systems Medicine and Digestive Diseases, Imperial College London, London, United Kingdom
| | | | | | | | | | | | | | - Tom Ross
- University of Tasmania, Hobart, Tasmania, Australia
| | - Iain L Chapple
- Periodontal Research Group, The University of Birmingham, Birmingham, United Kingdom
| | - William G Wade
- Centre for Host-Microbiome Interactions, King's College London, London, United Kingdom
| | | |
Collapse
|
43
|
Abstract
Integrated omics applied to microbial communities offers a great opportunity to analyze the niche breadths (i.e., resource and condition ranges usable by a species) of constituent populations, ranging from generalists, with a broad niche breadth, to specialists, with a narrow one. In this context, extracellular metabolomics measurements describe resource spaces available to microbial populations; dedicated analyses of metagenomics data serve to describe the fundamental niches of constituent populations, and functional meta-omics becomes a proxy to characterize the realized niches of populations and their variations though time or space. Thus, the combination of environmental omics and its thorough interpretation allows us to directly describe niche breadths of constituent populations of a microbial community, precisely and in situ This will greatly facilitate studies of the causes influencing ecosystem stability, resistance, and resilience, as well as generation of the necessary knowledge to model and predict the fate of any ecosystem in the current context of global change.
Collapse
|
44
|
Metagenome level metabolic network reconstruction analysis reveals the microbiome in the Bogotá River is functionally close to the microbiome in produced water. Ecol Modell 2019. [DOI: 10.1016/j.ecolmodel.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
45
|
Xu X, Zarecki R, Medina S, Ofaim S, Liu X, Chen C, Hu S, Brom D, Gat D, Porob S, Eizenberg H, Ronen Z, Jiang J, Freilich S. Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. ISME JOURNAL 2018; 13:494-508. [PMID: 30291327 DOI: 10.1038/s41396-018-0288-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/10/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022]
Abstract
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.
Collapse
Affiliation(s)
- Xihui Xu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.,Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Raphy Zarecki
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shlomit Medina
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Shany Ofaim
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.,Faculty of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Xiaowei Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chen Chen
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shunli Hu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dan Brom
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Daniella Gat
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Seema Porob
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Hanan Eizenberg
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Zeev Ronen
- Department of Environmental Hydrology and Microbiology, The Zuckerberg Institute for Water Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Sede-Boqer, 8499000, Israel
| | - Jiandong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.
| |
Collapse
|