mSystems, Journal Year: 2018, Volume and Issue: 3(2)
Published: March 19, 2018
Microbiomes underpin biogeochemical processes, sustain the bases of food webs, and recycle carbon nutrients. Thus, microbes are frontline players in determining ecosystem responses to environmental change.
Language: Английский
FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(6), P. 761 - 780
Published: July 25, 2018
Microbial networks are an increasingly popular tool to investigate microbial community structure, as they integrate multiple types of information and may represent systems-level behaviour. Interpreting these is not straightforward, the biological implications network properties unclear. Analysis allows researchers predict hub species interactions. Additionally, such analyses can help identify alternative states niches. Here, we review factors that result in spurious predictions address emergent be meaningful context microbiome. We also give overview studies analyse new hypotheses. Moreover, show a simulation how affected by choice environmental factors. For example, consistent across tools, heterogeneity induces modularity. highlight need for robust inference suggest strategies infer more reliably.
Language: Английский
Citations
472
Nature Microbiology, Journal Year: 2018, Volume and Issue: 3(8), P. 909 - 919
Published: July 18, 2018
Language: Английский
Citations
172
Environment International, Journal Year: 2021, Volume and Issue: 154, P. 106560 - 106560
Published: April 16, 2021
The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats human health, it is urgent develop efficient strategies eliminate them from Bacteria-driven PAE biodegradation been considered as an inexpensive yet effective strategy restore the contaminated Despite great advances in bacterial culturing and sequencing, inherent complexity indigenous microbial community hinders us mechanistically understand situ efficiently harness degrading power bacteria. synthetic ecology provides a simple controllable model system address this problem. In review, we focus on current progress mediated by isolates communities, discuss prospective PAE-degrading communities research. It anticipated that theories approaches will revolutionize study bacteria-driven provide novel insights for developing bioremediation solutions.
Language: Английский
Citations
121
Frontiers in Agronomy, Journal Year: 2022, Volume and Issue: 4
Published: June 30, 2022
Modern agriculture faces several challenges due to climate change, limited resources, and land degradation. Plant-associated soil microbes harbor beneficial plant growth-promoting (PGP) traits that can be used address some of these challenges. These are often formulated as inoculants for many crops. However, inconsistent productivity a problem since the performance individual inoculants/microbes vary with environmental conditions. Over past decade, ability utilize Next Generation Sequencing (NGS) approaches has led an explosion information regarding associated microbiomes. Although this type work been predominantly sequence-based descriptive in nature, increasingly it is moving towards microbiome functionality. The synthetic microbial communities (SynCom) approach emerging technique involves co-culturing multiple taxa under well-defined conditions mimic structure function microbiome. SynCom hopes increase community stability through synergistic interactions between its members. This review will focus on plant-soil-microbiome how they have potential improve crop production. Current formulation discussed, practical application considered.
Language: Английский
Citations
105
Food Research International, Journal Year: 2024, Volume and Issue: 188, P. 114497 - 114497
Published: May 11, 2024
Language: Английский
Citations
18
Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(40), P. 10124 - 10129
Published: Sept. 18, 2018
The rapid emergence of antibiotic-resistant pathogenic bacteria has accelerated the search for new antibiotics. Many clinically used antibacterials were discovered through culturing a single microbial species under nutrient-rich conditions, but in environment, constantly encounter poor nutrient conditions and interact with neighboring species. In an effort to recapitulate this we generated nine-strain actinomycete community 16S rDNA sequencing deconvolute stochastic production antimicrobial activity that was not observed from any axenic cultures. We subsequently simplified just two strains identified Amycolatopsis sp. AA4 as producing strain Streptomyces coelicolor M145 inducing strain. Bioassay-guided isolation amycomicin (AMY), highly modified fatty acid containing epoxide isonitrile warhead potent specific inhibitor Staphylococcus aureus . Amycomicin targets essential enzyme (FabH) biosynthesis reduces S. infection mouse skin-infection model. discovery AMY demonstrates utility screening complex communities against discover small-molecule
Language: Английский
Citations
90
Phytopathology, Journal Year: 2023, Volume and Issue: 113(8), P. 1369 - 1379
Published: March 1, 2023
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 overall understanding of microbial ecology in plant environment. As result, now, it possible to engineer consortium microbes aiming for health. Such synthetic communities (SynComs) contain carefully chosen species produce desired microbiome function. Microbial biofilm formation, production secondary metabolites, and ability induce resistance are some traits consider when designing SynComs. Plant-associated not assembled randomly. Ecological theories suggest that these defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study rules target functions generate phenotypes. Well-structured assemblages more likely lead stable SynCom thrives under environmental stressors as compared classical selection single activities or taxonomy. However, ensuring colonization long-term phenotype stability one challenges overcome SynComs, may change over time horizontal gene transfer retained mutations. Here, explored advances made research regarding health, focusing on bacteria, they most dominant form other members commonly found studies.
Language: Английский
Citations
36
Plant Stress, Journal Year: 2024, Volume and Issue: 14, P. 100632 - 100632
Published: Oct. 6, 2024
Language: Английский
Citations
12
The ISME Journal, Journal Year: 2018, Volume and Issue: 13(1), P. 92 - 103
Published: Aug. 16, 2018
Language: Английский
Citations
77
Applied and Environmental Microbiology, Journal Year: 2019, Volume and Issue: 85(8)
Published: Feb. 20, 2019
Isogenic bacterial populations are known to exhibit phenotypic heterogeneity at the single-cell level. Because of difficulties in assessing a single taxon mixed community, importance this deeper level organization remains relatively unknown for natural communities. In study, we have used membrane-based microcosms that allow probing while interacting with synthetic or community. Individual taxa were studied under axenic conditions, as members coculture physical separation, and culture. Phenotypic was assessed through both flow cytometry Raman spectroscopy. Using setup, investigated effect microbial interactions on individual heterogeneities two drinking water isolates. Through demonstrated between these bacteria lead reduction their diversities adjustment is conditional taxon. Single-cell spectroscopy confirmed taxon-dependent shift due interaction. conclusion, our data suggest may be general driver populations.IMPORTANCE Laboratory studies shown impact survival functionality isogenic populations. plays an important role pathogenicity virulence, antibiotic resistance, biotechnological applications, ecosystem properties, it crucial understand its influencing factors. An unanswered question whether communities influence community partners. We found coculturing leads heterogeneities, which led us hypothesis diversity dependent composition.
Language: Английский
Citations
41