Formation and emergent dynamics of spatially organized microbial systems DOI Creative Commons

Kelsey Cremin,

Sarah J. N. Duxbury,

Jerko Rosko

et al.

Interface Focus, Journal Year: 2023, Volume and Issue: 13(2)

Published: Feb. 10, 2023

Spatial organization is the norm rather than exception in microbial world. While study of physiology has been dominated by studies well-mixed cultures, there now increasing interest understanding role spatial physiology, coexistence and evolution. Where studied, shown to influence all three these aspects. In this mini review perspective article, we emphasize that dynamics within spatially organized systems (SOMS) are governed feedbacks between local physico-chemical conditions, cell movement, These can give rise emergent dynamics, which need be studied through a combination spatio-temporal measurements mathematical models. We highlight initial formation SOMS their as two open areas investigation for future studies. will benefit from development model mimic natural ones terms species composition structure.

Language: Английский

Recent advances in biological approaches towards anode biofilm engineering for improvement of extracellular electron transfer in microbial fuel cells DOI Open Access
Tahseena Naaz,

Ankit Kumar,

Anusha Vempaty

et al.

Environmental Engineering Research, Journal Year: 2023, Volume and Issue: 28(5), P. 220666 - 0

Published: Jan. 10, 2023

Over the last two decades, scientific communities have been more interested in turning organic waste materials into bioenergy. Microbial fuel cells (MFC) can degrade wastewater and produce electrical power. Many constraints limited development of MFC. Among them, anode biofilm is one significant that need to be improved. This review delineates role various biological components electroactive biofilm. The current article focuses on numerous electron exchange methods for microbiome-induced transfer activity, different proteins, secretory chemicals involved transfer. study also several proteomics genomics methodologies adopted developed improve extra mechanism bacteria. Recent advances publications synthetic biology genetic engineering investigating direct indirect transport phenomena highlighted. helps reader understand recent manipulations biofilm, electrode material modifications, EET mechanisms, operational strategies improving performance. discusses challenges present technology future direction production at anode.

Language: Английский

Citations

62
Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation DOI Creative Commons
Uli Klümper, Giulia Gionchetta, Elisa Catão

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: June 8, 2024

Abstract When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat’s microbiome in long term if are able to overcome biotic resilience towards immigration. This process should more difficult with increasing biodiversity, as exploitable niches a given habitat reduced for immigrants when diverse competitors present. Consequently, microbial diversity could provide natural barrier resistance by reducing persistence time immigrating ARB ARG. To test this hypothesis, pan-European sampling campaign was performed structured forest soil dynamic riverbed environments low anthropogenic impact. In soils, higher diversity, evenness richness were significantly negatively correlated relative abundance >85% ARGs. Furthermore, number detected ARGs per sample inversely diversity. However, no such effects present riverbeds. Hence, serve dissemination stationary, environments, where long-term, diversity-based against immigration evolve.

Language: Английский

Citations

23
A metagenomic perspective on the microbial prokaryotic genome census DOI Creative Commons
Dongying Wu, R. Seshadri, Nikos C. Kyrpides

et al.

Science Advances, Journal Year: 2025, Volume and Issue: 11(3)

Published: Jan. 17, 2025

Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) >1.5 million microbial genomes in public databases, including metagenome-assembled (MAGs) uncultivated microbes. As compared to vast uncovered by metagenomic sequences, cultivated taxa account for a modest portion overall diversity, 9.73% bacteria and 6.55% archaea, while MAGs contribute 48.54% 57.05%, respectively. Therefore, substantial fraction bacterial (41.73%) archaeal PD (36.39%) still lacks any genomic representation. This unrepresented manifests primarily at lower taxonomic ranks, exemplified 134,966 species identified 18,087 samples. Our study exposes hotspots freshwater, marine subsurface, sediment, soil, other environments, whereas human samples yielded minimal novelty within context existing datasets. These results offer roadmap future genome recovery efforts, delineating uncaptured underexplored environments underscoring necessity renewed isolation sequencing.

Language: Английский

Citations

5
Threats of antibiotic resistance: an obliged reappraisal DOI Open Access
Fernando Baquero

International Microbiology, Journal Year: 2021, Volume and Issue: 24(4), P. 499 - 506

Published: May 24, 2021

Language: Английский

Citations

78
Evolutionary Pathways and Trajectories in Antibiotic Resistance DOI
Fernando Baquero, José Luis Martínez, Val F. Lanza

et al.

Clinical Microbiology Reviews, Journal Year: 2021, Volume and Issue: 34(4)

Published: June 30, 2021

Evolution is the hallmark of life. Descriptions evolution microorganisms have provided a wealth information, but knowledge regarding "what happened" has precluded deeper understanding "how" proceeded, as in case antimicrobial resistance. The difficulty answering question lies multihierarchical dimensions evolutionary processes, nested complex networks, encompassing all units selection, from genes to communities and ecosystems. At simplest ontological level (as resistance genes), proceeds by random (mutation drift) directional (natural selection) processes; however, sequential pathways adaptive variation can occasionally be observed, under fixed circumstances (particular fitness landscapes), predictable. highest (such that plasmids, clones, species, microbiotas), systems' degrees freedom increase dramatically, related variable dispersal, fragmentation, relatedness, or coalescence bacterial populations, depending on heterogeneous changing niches selective gradients environments. Evolutionary trajectories antibiotic find their way these landscapes subjected variations, becoming highly entropic therefore unpredictable. However, experimental, phylogenetic, ecogenetic analyses reveal preferential frequented paths (highways) where flows propagates, allowing some dynamics, modeling designing interventions. Studies an applied aspect improving individual health, One Health, Global well academic value for evolution. Most importantly, they heuristic significance model reduce negative influence anthropogenic effects environment.

Language: Английский

Citations

73
Pseudomonas aeruginosa: an antibiotic resilient pathogen with environmental origin DOI Creative Commons
Pablo Laborda, Fernando Sanz‐García, Sara Hernando‐Amado

et al.

Current Opinion in Microbiology, Journal Year: 2021, Volume and Issue: 64, P. 125 - 132

Published: Oct. 26, 2021

Pseudomonas aeruginosa, a bacterium characterized for its low antibiotics' susceptibility, is one of the most relevant opportunistic pathogens, causing infections at hospitals and in cystic fibrosis patients. Besides relevance human health, P. aeruginosa colonizes environmental ecosystems; therefore elements driving infectivity antibiotic resistance must be analyzed from One-Health perspective. Although some epidemic clones have been described, there are not specific lineages linked to infections, suggesting that virulence determinants evolved nature play functions other than infecting host avoiding antimicrobial treatment. Herein, we review current information on population structure functional role non-clinical ecosystems.

Language: Английский

Citations

57
The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples DOI Creative Commons
Mitchell T. Caudill, Kelly A. Brayton

Microorganisms, Journal Year: 2022, Volume and Issue: 10(3), P. 605 - 605

Published: March 12, 2022

With the advent of cheaper, high-throughput sequencing technologies, ability to survey biodiversity in previously unexplored niches and geographies has expanded massively. Within Anaplasma, a genus containing several intra-hematopoietic pathogens medical economic importance, at least 25 new species have been proposed since last formal taxonomic organization. Given obligate intracellular nature these bacteria, none able attain standing nomenclature per International Code Nomenclature Prokaryotes rules. Many novel species' proposals use sequence data obtained from targeted or metagenomic PCR studies only few genes, most commonly 16S rRNA gene. We examined utility gene for discriminating Anaplasma samples level. find that while genetic diversity appears greater than appreciated organization genus, caution must be used when attempting resolve descriptor alone. Specifically, genomically distinct similar sequences, especially partial amplicons are used. Furthermore, we provide key bases allow classification formally named Anaplasma.

Language: Английский

Citations

45
Ecology of the respiratory tract microbiome DOI Open Access
Ana Elena Pérez‐Cobas, Jerónimo Rodríguez-Beltrán, Fernando Baquero

et al.

Trends in Microbiology, Journal Year: 2023, Volume and Issue: 31(9), P. 972 - 984

Published: May 10, 2023

Language: Английский

Citations

23
Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau DOI Creative Commons
Bo Wei, Qianqian Xu,

Junfei Kong

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Feb. 21, 2025

Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays critical role in livestock production and grassland restoration. This study investigates rhizospheric non-rhizospheric soil microorganisms of L. Ganzi River area Qinghai Lake basin using metagenomic sequencing to understand their diversity potential ecological functions. Soil samples were collected from areas S-type five-point sampling method. DNA was extracted, performed BGISEQ-500 platform. Alpha Beta analyses conducted, LEfSe analysis used identify differentially abundant microbial taxa metabolic pathways. A total 5,681 species across 1,606 genera, 521 families, 61 phyla, 246 orders identified. Non-rhizospheric soils exhibited higher richness than soils. Proteobacteria most phylum both types. Rhizospheric showed significant enrichment pathways related antibiotic biosynthesis, carbon metabolism, methane while enriched quorum sensing drug-metabolizing The findings highlight selective influence communities mitigating emissions. provides foundation for understanding functions alpine meadows supports sustainable management practices.

Language: Английский

Citations

1
The interactions between oral-gut axis microbiota and Helicobacter pylori DOI Creative Commons
Xi Chen, Nanxi Wang, Jiannan Wang

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: Aug. 3, 2022

In the human body, each microbial habitat exhibits a different population pattern, and these distinctive microflorae are highly related to development of diseases. The interactions from host niches becoming crucial regulators shape microbiota their physiological or pathological functions. oral cavity gut most complex interdependent habitats. Helicobacter pylori is one important pathogens digestive tract, especially stomach, due its direct relationships with many gastric diseases including cancer. H. infections can destroy normal environment make stomach livable channel enhance between gut, thus reshaping microbiomes. be also detected in while interaction oral-gut axis plays major role ’s colonization, infection, pathogenicity. Both infection eradication alter balance microecology axis, which affect occurrence progress shift maybe potential targets for infectious diagnosis treatment.

Language: Английский

Citations

33