Baseline microbiome composition impacts resilience to and recovery following antibiotics DOI Creative Commons
Chia‐Yu Chen, Ulrike Löber, Hendrik Bartolomaeus

et al.

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

Published: March 31, 2024

The gut microbiome of healthy individuals naturally undergoes temporal changes linked to the dynamics its community components 1 . These are only observable in longitudinal studies; they particularly relevant understanding ecosystem responses external environment disturbances. External exposures, such as antibiotic treatment, significantly reshape microbiome, impacting both pathogen and commensal microbes 2 plays pivotal roles digestion, nutrient absorption, mental health, influencing immune systems, obesity, various diseases 3-6 Consequently, beyond short-term effects on host dynamics, alterations resulting from exposure also have enduring repercussions human health physiological equilibrium 7 Therefore, enhancing resilience during treatment is essential, with goal mitigating prolonged adverse effects. Here, we explored impact pre-antibiotic microbial functional profiles resilience, suggesting that specific baseline features exhibit greater antibiotics-induced changes. Our results identified an uncultured Faecalibacterium prausnitzii taxon a species at associated diminished resilience. We demonstrated this association could be role F. keystone species. Additionally, observed influence other bacteria, Bifidobacterium animalis Lactobacillus acidophilus , well modules, multidrug resistance efflux pump, This lays foundations for designing targeted strategies promote resilient before alleviating possible health.

Language: Английский

Soil microbial diversity plays an important role in resisting and restoring degraded ecosystems DOI
Alexandre Pedrinho, Lucas William Mendes, Arthur Prudêncio de Araújo Pereira

et al.

Plant and Soil, Journal Year: 2024, Volume and Issue: 500(1-2), P. 325 - 349

Published: Jan. 30, 2024

Language: Английский

Citations

30
Strategies for tailoring functional microbial synthetic communities DOI Creative Commons
Jiayi Jing, Paolina Garbeva, Jos M. Raaijmakers

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity soil microorganisms their complex interactions make it challenging to pinpoint the main players life support functions can provide plants, including enhanced tolerance (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity unravel molecular chemical basis interplay specific microbiome functions. While SynComs have been successfully employed dissect or reproduce microbiome-associated phenotypes, assembly reconstitution these often based on generic abundance patterns taxonomic identities co-occurrences but only rarely informed by functional traits. Here, we review recent studies designing reveal common principles discuss multidimensional approaches community design. We propose strategy tailoring design integration high-throughput experimental assays with strains computational genomic analyses capabilities.

Language: Английский

Citations

26
Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef DOI Creative Commons

Marko Terzin,

Steven J. Robbins, Sara C. Bell

et al.

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: Jan. 16, 2025

Language: Английский

Citations

1
Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding DOI Creative Commons
Peter Contos, Heloise Gibb, Nicholas P. Murphy

et al.

Journal of Environmental Management, Journal Year: 2025, Volume and Issue: 375, P. 124344 - 124344

Published: Feb. 1, 2025

Restoring degraded ecosystems is a complex process that involves rebuilding myriad species interactions make functioning ecological community. Microorganisms are key to robust restoration - their mutualisms with above-ground communities drive community assembly and increase host fitness. However, microbes largely ignored during there significant knowledge gap regarding how restore communities. Here, we tested whether could enhance between invertebrate hosts by reintroducing, or 'rewilding', leaf litter soil from remnant sites containing species-rich microbial communities, into poor geographically isolated revegetated farmland sites. We sequenced both the microbiome gut of two dominant invertebrates: native Ecnolagria grandis beetles introduced Ommatoiulus moreleti millipedes. sampled 35 months after initial reintroduction event in (conservation area source transplant), rewilding transplant (revegetation site control no transplant). found even ∼20 years revegetation, had distinct compared areas. Although transplants failed similarity towards sites, marked increases diversity richness E. microbiomes greater degree overlap within relative In contrast, were few changes O. microbiomes. Overall, our results suggest can recover some but may not influence all host-microbe systems.

Language: Английский

Citations

1
Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance DOI Creative Commons
Samuel E. Barnett, Ashley Shade

Ecology Letters, Journal Year: 2024, Volume and Issue: 27(3)

Published: March 1, 2024

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems their functions. Many critical ecosystem functions, such as biogeochemical cycling, facilitated by microbial communities. Understanding functional consequences of microbiome responses to press requires ongoing observations active populations that contribute This study leverages a 7-year time series 60-year-old coal seam fire (Centralia, Pennsylvania, USA) examine resilience soil bacterial microbiomes disturbance. Using 16S rRNA gene amplicon sequencing, we assessed interannual dynamics subset 'whole' community. Contrary our hypothesis, whole communities demonstrated greater than subsets, suggesting inactive members contributed overall structural resilience. Thus, in addition selection mechanisms populations, perceived is also supported dispersal, persistence, revival from local dormant pool.

Language: Английский

Citations

7
Tourism as a catalyst for resilience: Strategies for building sustainable and adaptive communities DOI
Mohamed Khater,

Mohamed Faik

Community Development, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 17

Published: July 27, 2024

Tourism is increasingly recognized as a vital force for resilience, offering communities the chance to develop sustainable and adaptable systems amidst various challenges. This research explores link between tourism community focusing on ways enhance resilience through activities. By reviewing existing literature case studies, we assess how supports economic, environmental, social, cultural resilience. The findings show that essential diversifying economies, promoting environmental sustainability, preserving heritage, fostering social inclusion. However, issues like over-tourism, harm, commodification hinder resilience-building. To address these, propose strategies policymakers, planners, stakeholders integrate principles into development. These include tourism, increasing engagement, forming partnerships collaborative initiatives. leveraging tourism's transformative potential, can strengthen their ensuring long-term sustainability adaptability in changing world.

Language: Английский

Citations

7
Microbial functional diversity and redundancy: moving forward DOI Creative Commons
Pierre Ramond, Pierre E. Galand, Ramiro Logares

et al.

FEMS Microbiology Reviews, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract Microbial functional ecology is expanding as we can now measure the traits of wild microbes that affect ecosystem functioning. Here, review techniques and advances could be bedrock for a unified framework to study microbial functions. These include our newfound access environmental genomes, collections traits, but also ability microbes’ distribution expression. We then explore technical, ecological, evolutionary processes explain patterns diversity redundancy. Next, suggest reconciling microbiology with biodiversity-ecosystem-functioning studies by experimentally testing significance redundancy efficiency, resistance, resilience processes. Such will aid in identifying state shifts tipping points microbiomes, enhancing understanding how where microbiomes guide Earth's biomes context changing planet.

Language: Английский

Citations

4
Potassium mediates succession of microbial community and nitrogen functions under long-term sloping cultivation with soybean DOI
Zhijun Chen, Kai Zhang, Fangli Su

et al.

Agriculture Ecosystems & Environment, Journal Year: 2025, Volume and Issue: 382, P. 109466 - 109466

Published: Jan. 15, 2025

Language: Английский

Citations

0
Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures DOI Creative Commons

Mxolisi Nene,

Nokuthula Winfred Kunene,

Rian Pierneef

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: Feb. 4, 2025

Introduction The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. gut microbiome plays a critical role in supporting this by influencing health and productivity. This study aimed investigate the diversity functional capacities faecal from Limpopo KwaZulu-Natal provinces South Africa. Methods Using combination 16S rRNA gene sequencing shotgun metagenomic technologies, we analysed 98 72 datasets. Taxonomic profiles annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), potential zoonotic pathogens. Results analysis showed that predominant phyla both Firmicutes, Bacteroidota, Proteobacteria, Actinobacteria. At genus level, Escherichia Shigella prevalent, with coli dysenteriae identified as major contributors microbiome. ARGs identified, MarA , PmrF AcrE detected KwaZulu-Natal, cpxA mdtG, TolA Limpopo. These primarily mediate efflux alteration. Discussion detection bacteria such S treptococcus spp. highlights risks humans through food chain, emphasizing importance improved household hygiene practices. underscores chicken adaptability, linking efficiency settings. Targeted interventions further research are crucial for mitigating enhancing sustainability farming.

Language: Английский

Citations

0
A test for microbiome-mediated rescue via host phenotypic plasticity in Daphnia DOI
René S. Shahmohamadloo,

Amir R. Gabidulin,

Ellie R. Andrews

et al.

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2044)

Published: April 1, 2025

Phenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often change considerably environmental variation, and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it unclear whether changes microbiome composition contribute limiting our knowledge of underlying mechanisms and, ultimately, fate inhabiting changing environments. In this study, we examined responses 20 genetically distinct Daphnia magna genotypes exposed non-toxic toxic diets containing Microcystis , cosmopolitan cyanobacterium common stressor for Daphnia. exhibited significant survival, reproduction population growth rates upon exposure . effects on were limited, with effect being differences abundance observed across five bacterial families. Moreover, there was no correlation between magnitude plasticity. Our results suggest that played negligible role driving microbiome-mediated rescue.

Language: Английский

Citations

0