Community standards and future opportunities for synthetic communities in plant–microbiota research

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(11), P. 2774 - 2784

Published: Oct. 30, 2024

Language: Английский

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Microbial interactions in theory and practice: when are measurements compatible with models?

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 75, P. 102354 - 102354

Published: July 6, 2023

Most predictive models of ecosystem dynamics are based on interactions between organisms: their influence each other’s growth and death. We review here how theoretical approaches used to extract interaction measurements from experimental data in microbiology, particularly focusing the generalised Lotka–Volterra (gLV) framework. Though widely used, we argue that gLV model should be avoided for estimating batch culture — most common, simplest cheapest vitro approach culturing microbes. Fortunately, alternative offer a way out this conundrum. Firstly, side, alternatives such as serial-transfer chemostat systems more closely match assumptions model. Secondly, explicit organism-environment can study batch-culture systems. hope our recommendations will increase tractability microbial experimentalists theoreticians alike.

Language: Английский

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From microbiome composition to functional engineering, one step at a time

Microbiology and Molecular Biology Reviews, Journal Year: 2023, Volume and Issue: 87(4)

Published: Nov. 10, 2023

SUMMARY Communities of microorganisms (microbiota) are present in all habitats on Earth and relevant for agriculture, health, climate. Deciphering the mechanisms that determine microbiota dynamics functioning within context their respective environments or hosts (the microbiomes) is crucially important. However, sheer taxonomic, metabolic, functional, spatial complexity most microbiomes poses substantial challenges to advancing our knowledge these mechanisms. While nucleic acid sequencing technologies can chart composition with high precision, we mostly lack information about functional roles interactions each strain a given microbiome. This limits ability predict microbiome function natural and, case dysfunction dysbiosis, redirect onto stable paths. Here, will discuss systematic approach (dubbed N + 1/N−1 concept) enable step-by-step dissection assembly functioning, as well intervention procedures introduce eliminate one particular microbial at time. The N+1/N−1 concept informed by invasion events selects culturable, genetically accessible microbes well-annotated genomes proliferation decline defined synthetic and/or complex microbiota. enables harnessing classical microbiological diversity approaches, omics tools mathematical modeling decipher underlying outcomes. Application this further provides stepping stones benchmarks structure analyses more strategies.

Language: Английский

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Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Database, Journal Year: 2023, Volume and Issue: 2023

Published: Jan. 1, 2023

Abstract Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function evolution facilitate genomic selection. These datasets hold immense value for both current future studies, as they are vital crop breeding, yield improvement overall agricultural sustainability. However, integrating these from heterogeneous sources presents significant challenges hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 a part of AgBioData Consortium (https://www.agbiodata.org) review types resources that support archiving, analysis visualization needs plant research community. For 2021–22, we identified different examined metadata annotations related experimental design/methods/sample collection, etc. Furthermore, thoroughly reviewed publicly funded repositories raw processed well secondary databases knowledgebases enable integration context genome browser, pathway networks tissue-specific expression. Based on our survey, recommend need (i) additional infrastructural archiving many new types, (ii) development community standards annotation formatting, (iii) biocuration (iv) tools connect with enhance knowledge synthesis foster translational research. Although this paper only covers relevant community, expect similar issues shared by researchers working animals. Database URL: https://www.agbiodata.org.

Language: Английский

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When biodiversity preservation meets biotechnology: The challenge of developing synthetic microbiota for resilient sustainable crop production

Journal of Sustainable Agriculture and Environment, Journal Year: 2023, Volume and Issue: 2(1), P. 5 - 15

Published: Feb. 7, 2023

Abstract Agriculture needs to develop novel strategies and practices meet the increasing global food demand, in an ecological economical sustainable framework. The plant‐associated microbiota is gaining attention as part of these since it strongly contributes plant health, nutrition, resilience environmental perturbations. However, domestication has brought reduction abilities recruit a beneficial microbiota. It becoming clear that successful use requires multifaceted approach where microbiologist, geneticists, scientists, agronomists, computational biologists can ways solutions modify both plant's ability it, directed increase crop performances. Here, while briefly reviewing state‐of‐the‐art research, we focus on need discover, understand associated with wild relatives crops neglected crops, which harbour biodiversity needed for developing efficient bioinoculant solutions. In particular, emphasize convergence situ preservation microbiome preservation, provides added value nature habitat conservation, living collections biodiversity. heuristic bioinoculants (viz., synthetic communities) proper models predict outcome their applications also discussed toward systems‐biology‐guided development.

Language: Английский

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Interactions between bacteria in the human nasopharynx: a scoping review

The Lancet Microbe, Journal Year: 2025, Volume and Issue: unknown, P. 101062 - 101062

Published: March 1, 2025

Emerging evidence indicates that interactions between bacteria shape the nasopharyngeal microbiome and influence respiratory health. This Review uses systematic scoping methodology to summarise 88 studies including observational experimental studies, identifying key colonise human nasopharynx. A range of bacterial were reported in a variable association Streptococcus pneumoniae Haemophilus influenzae, consistent positive S Moraxella catarrhalis, negative Staphylococcus aureus. Experimental largely validated associations provided insights into mechanism direction interactions. In context health, non-pneumococcal alpha-haemolytic streptococci Gram-positive commensals Dolosigranulum Corynebacterium inhibited pathogens such as H pneumoniae, M These findings underscore how competition coexistence composition this niche. study has relevance for health can be helpful informing design potential microbiota-targeted therapies.

Language: Английский

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Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

mSystems, Journal Year: 2023, Volume and Issue: unknown

Published: June 20, 2023

Microbes commonly organize into communities consisting of hundreds species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles these microbial communities. These snapshots, when collected from multiple samples, can co-occurrence microbes, providing a glimpse network associations However, inference networks data involves numerous steps, requiring specific tools parameter choices. Moreover, extent to which steps affect final is still unclear. In this study, we perform meticulous analysis step pipeline convert sequencing associations. Through process, map how different choices algorithms parameters identify contribute substantially variance. We further determine generate robust develop consensus based on benchmarks mock synthetic sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows default help explore outcome combinations inferred networks. envisage could be used for integrating sets generating comparative analyses guide our understanding community assembly biomes. IMPORTANCE Mapping interrelationships between important controlling their structure function. surge high-throughput has led creation thousands containing information about abundances. abundances transformed networks, within microbiomes. processing obtain relies several corresponding parameters. options pose questions robustness uniqueness address workflow provide systematic guidelines appropriate tool selection particular set. also algorithm helps more benchmark

Language: Английский

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Resolving metabolic interaction mechanisms in plant microbiomes

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 74, P. 102317 - 102317

Published: April 14, 2023

Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those plants. However, disentangling molecular basis these their specific roles remains a major challenge. Here, we review recent applications experimental computational methods toward elucidation metabolic in plant-associated microbiomes. We highlight studies that span various scales taxonomic environmental complexity, test interaction outcomes vitro planta by deconstructing microbial communities. also discuss how continued integration multiple can further reveal general ecological characteristics plant as well provide strategies for areas such improved protection, bioremediation, sustainable agriculture.

Language: Английский

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Inferring Bacterial Interspecific Interactions from Microcolony Growth Expansion

microLife, Journal Year: 2024, Volume and Issue: 5

Published: Jan. 1, 2024

Bacterial species interactions significantly shape growth and behavior in communities, determining the emergence of community functions. Typically, these are studied through bulk population measurements, overlooking role cell-to-cell variability spatial context. This study uses real-time surface measurements thousands sparsely positioned microcolonies to investigate kinetic variations monocultures cocultures

Language: Английский

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Agricultural Sciences in the Big Data Era: Genotype and Phenotype Data Standardization, Utilization and Integration

Published: June 14, 2023

The Genotype-Phenotype Working Group was established in November 2021 as part of the AgBioData Consortium (https://www.agbiodata.org) with goal identifying current challenges annotating and integrating large-scale genotype phenotype data. Over course year, members this working group identified different types data sets, explored experimental platforms methods for generation, examined how these are annotated including metadata requirements. We conducted a thorough review publicly funded repositories raw processed each type. also several secondary databases knowledgebases that enable integration heterogeneous context Genome Browser, Pathway Networks tissue-specific gene expression. revealed need additional infrastructural support, standards, tools to connect Genotype Phenotype enhance interoperability knowledge synthesis foster translational research.

Language: Английский

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