Integrating natural language processing and genome analysis enables accurate bacterial phenotype prediction DOI Creative Commons
Daniel Gómez‐Pérez, Alexander Keller

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

Abstract Understanding microbial phenotypes from genomic data is crucial in areas of research including co-evolution, ecology and pathology. This study proposes a new approach to integrate literature-derived information with traits, combining natural language processing (NLP) functional genome analysis. We applied this methodology publicly available overcome current limitations provide novel insights into phenotype prediction. fine-tuned specialized transformer-based large models analyze 3.3 million open-access scientific articles, extracting network phenotypic linked bacterial strains. The maps relationships between strains traits such as pathogenicity, metabolic capacity, host biome preference. By functionally annotating reference assemblies for the network, we were able predict key genes influencing phenotypes. Our findings align known reveal correlations, leading identification relevant particular disease host-association interconnectivity within provided further understanding community interactions, hub species by inferring trophic connections—insights challenging extract means experimental work. demonstrates potential machine learning methods uncover cross-species patterns gene-phenotype correlations. As number sequenced literature descriptions grows exponentially, become meaningful advancing microbiology research.

Language: Английский

Co‐evolution within the plant holobiont drives host performance DOI Creative Commons
Fantin Mesny, Stéphane Hacquard, Bart P. H. J. Thomma

et al.

EMBO Reports, Journal Year: 2023, Volume and Issue: 24(9)

Published: July 20, 2023

Plants interact with a diversity of microorganisms that influence their growth and resilience, they can therefore be considered as ecological entities, namely "plant holobionts," rather than singular organisms. In plant holobiont, the assembly above- belowground microbiota is ruled by host, microbial, environmental factors. Upon microorganism perception, plants activate immune signaling resulting in secretion factors modulate composition. Additionally, metabolic interdependencies antagonism between microbes are driving forces for community assemblies. We argue complex plant-microbe intermicrobial interactions have been selected during evolution may promote survival fitness associated holobionts. As part this process, evolved metabolite-mediated strategies to selectively recruit beneficial microbiota. Some these members show host-adaptation, from which mutualism rapidly arise. also co-evolved antagonistic activities restrict proliferation high pathogenic potential prevent disease development. Co-evolution within holobionts thus ultimately drives performance.

Language: Английский

Citations

61
Methods for screening and evaluation of antimicrobial activity: A review of protocols, advantages, and limitations DOI Open Access
Tanim Jabid Hossain

European Journal of Microbiology and Immunology, Journal Year: 2024, Volume and Issue: 14(2), P. 97 - 115

Published: April 22, 2024

Abstract Infectious diseases pose a formidable global challenge, compounded by the emergence of antimicrobial resistance. Consequently, researchers are actively exploring novel compounds as potential solutions. This endeavor underscores pivotal role methods employed for screening and evaluating activity—a critical step in discovery characterization agents. While traditional techniques such well-diffusion, disk-diffusion, broth-dilution commonly utilized assays, they may encounter limitations concerning reproducibility speed. Additionally, diverse array assays including cross-streaking, poisoned-food, co-culture, time-kill kinetics, resazurin assay, bioautography, etc., routinely evaluations. Advanced flow-cytometry, impedance analysis, bioluminescent technique offer rapid sensitive results, providing deeper insights into impact antimicrobials on cellular integrity. However, their higher cost limited accessibility certain laboratory settings present challenges. article provides comprehensive overview designed to characterize activity, elucidating underlying principles, protocols, advantages, limitations. The primary objective is enhance understanding methodologies agents our relentless battle against infectious diseases. By selecting appropriate testing method, can discern suitable conditions streamline identification effective

Language: Английский

Citations

57
Deep discovery informs difficult deployment in plant microbiome science DOI Creative Commons
Dor Russ, Connor R. Fitzpatrick, Paulo José Pereira Lima Teixeira

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(21), P. 4496 - 4513

Published: Oct. 1, 2023

Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to productivity. The basic definition of across species ecosystems, combined with the development reductionist experimental models manipulation phenotypes microbes, has fueled interest in its translation agriculture. However, great majority microbes exhibiting plant-productivity traits lab greenhouse fail field. Therapeutic must reach détente, establishment uneasy homeostasis, system, invade heterogeneous pre-established plant-associated communities, persist a new potentially remodeled community. Environmental conditions alter community structure thus impact engraftment therapeutic microbes. We survey recent breakthroughs, challenges, opportunities translating from

Language: Английский

Citations

53
Microbiome-mediated plant disease resistance: recent advances and future directions DOI Creative Commons
Yulin Du,

Xiaowei Han,

Kenichi Tsuda

et al.

Journal of General Plant Pathology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

Abstract Plant pathogens cause plant diseases that significantly decrease crop yields, posing a serious threat to global food security. While disease resistance has traditionally been understood as the trait determined by innate immune system and pathogen virulence system, recent research underscores pivotal role of microbiome in resistance. Plant-associated microbiomes confer protection against through direct inhibition, resource competition, activation responses. Agricultural practices such rotation, intercropping, disease-resistant breeding, biocontrol, organic farming modulate microbiomes, thereby influencing This review synthesizes latest advancements understanding intricate interactions among plants, pathogens, microbiomes. We emphasize need for in-depth mechanistic studies linking agricultural dynamics propose future directions leverage sustainable agriculture.

Language: Английский

Citations

6
Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms DOI Creative Commons
Liese Vlasselaer, Sam Crauwels, Bart Lievens

et al.

FEMS Microbiology Ecology, Journal Year: 2024, Volume and Issue: 100(3)

Published: Feb. 2, 2024

Abstract Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health productivity. While microbiomes of soil-bound cultivated crops are extensively studied, hydroponically have received limited attention. To address this knowledge gap, we investigated rhizosphere root endosphere lettuce. Additionally, sought to explore potential impact oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic nonsymptomatic in three different greenhouses. Amplicon sequencing bacterial 16S rRNA gene revealed significant alterations community upon P. infection, particularly rhizosphere. Permutational multivariate analysis variance (perMANOVA) differences microbial communities greenhouses, plants. Further uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) Interestingly, members Pseudomonas Flavobacterium positively with Overall, study provides valuable insights into microbiome highlights influence invasion plant-associated communities. research required elucidate role spp. controlling infections within lettuce

Language: Английский

Citations

4
The chemical language of plant–microbe–microbe associations: an introduction to a Virtual Issue DOI
Stéphane Hacquard, Francis Martin

New Phytologist, Journal Year: 2024, Volume and Issue: 244(3), P. 739 - 742

Published: Oct. 2, 2024

This Editorial introduces the Virtual Issue ‘Chemical language of plant–microbe–microbe associations’ that includes following papers: Basak et al . (2024), Böttner (2023), Brisson Feng Gfeller Gómez‐Pérez Hong (2022, 2023), Hu Jiang Lee Nakano Ökmen Revillini Rovenich & Thomma Simonin (2022), Snelders Walsh Wen Xia Xie Zhang (2023, 2024), Zheng Zhou 2024). Access at www.newphytologist.com/virtualissues

Language: Английский

Citations

4
AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins DOI Creative Commons
Fantin Mesny, Bart P. H. J. Thomma

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 4, 2024

Abstract Fungi typically occur in environments where numerous and diverse other microbes as well, often resulting fierce competition for nutrients habitat. To support fungal fitness these environments, they evolved various mechanisms that mediate direct antagonism towards niche competitors. Among these, the secretion of proteins with antimicrobial activities has been reported fungi lifestyles. Recently, several plant-associated were shown to rely on effector antagonize certain members plant hosts’ microbiota successfully colonize tissues. Some effectors do not share homology known antimicrobials represent novel antibiotics. Accordingly, occurrence conservation proteinaceous throughout tree life remains enigmatic. Here we present a computational approach annotate candidate secretomes based protein physicochemical properties. After curating set experimentally verified display activity lack such activity, trained machine learning classifier properties sequences predicted structures. This predictor performs particularly well (R 2 =0.89) according our validations is delivered software package named AMAPEC, dedicated nti m icrobial ctivity p rediction e ffector c andidates. We subsequently used this predict catalogs three phylogenetically distant distinct lifestyles, revealing relatively large each fungi, suggesting broad kingdom. Thus, AMAPEC unique method uncover are sparsely functionally annotated, may assist biological interpretations during omic analyses. It freely available at https://github.com/fantin-mesny/amapec .

Language: Английский

Citations

2
The impact of filamentous plant pathogens on the host microbiota DOI Creative Commons
Víctor M. Flores‐Núñez, Eva H. Stukenbrock

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Aug. 15, 2024

Abstract When a pathogen invades plant, it encounters diverse microbiota with some members contributing to the health and growth of plant host. So far, relevance interactions between pathogens are poorly understood; however, new lines evidence suggest that play an important role in shaping microbiome their host during invasion. This review aims summarize recent findings document changes microbial community composition invasion filamentous tissues. We explore known mechanisms interaction underlie these changes, particularly pathogen-encoded traits produced target specific microbes. Moreover, we discuss limitations current strategies shed light on perspectives study complex networks microbiome.

Language: Английский

Citations

2
Meddling with the microbiota: Fungal tricks to infect plant hosts DOI Creative Commons
Fantin Mesny,

Martha Bauer,

Jinyi C. Zhu

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102622 - 102622

Published: Sept. 5, 2024

Language: Английский

Citations

2
Battle of the bugs: how an oomycete pathogen shapes the microbiota of its host DOI Creative Commons
Hanna Rövenich, Bart P. H. J. Thomma

New Phytologist, Journal Year: 2023, Volume and Issue: 239(6), P. 2064 - 2066

Published: July 10, 2023

This article is a Commentary on Gómez‐Pérez et al . (2023), 239 : 2320–2334

Language: Английский

Citations

2