Innovations to culturing the uncultured microbial majority

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 19(4), P. 225 - 240

Published: Oct. 22, 2020

Language: Английский

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Gut microbiota in colorectal cancer development and therapy

Nature Reviews Clinical Oncology, Journal Year: 2023, Volume and Issue: 20(7), P. 429 - 452

Published: May 11, 2023

Language: Английский

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Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer

Cancer Cell, Journal Year: 2022, Volume and Issue: 40(2), P. 153 - 167.e11

Published: Feb. 1, 2022

Language: Английский

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High-throughput microbial culturomics using automation and machine learning

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(10), P. 1424 - 1433

Published: Feb. 20, 2023

Abstract Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale lack phenotype–genotype integration. Here we describe an open-source high-throughput robotic strain isolation platform the rapid generation of isolates on demand. We develop a machine learning approach that leverages colony morphology genomic data maximize diversity microbes isolated enable targeted picking specific genera. Application this fecal samples 20 humans yields personalized gut biobanks totaling 26,997 represented >80% all abundant taxa. Spatial analysis >100,000 visually captured colonies reveals cogrowth patterns between Ruminococcaceae , Bacteroidaceae Coriobacteriaceae Bifidobacteriaceae families suggest important interactions. Comparative 1,197 high-quality genomes these shows interesting intra- interpersonal evolution, selection horizontal gene transfer. This culturomics framework should empower new research efforts systematize collection quantitative imaging-based phenotypes with high-resolution genomics many emerging studies.

Language: Английский

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Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors

BMC Microbiology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Feb. 21, 2023

Abstract Background The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles these ecosystems, particularly degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function not yet well understood as most species have isolated axenic cultures. Here we used metagenomic approach to investigate diversity metabolic potential three environmentally different bioreactors: methanogenic full-scale reactor, activated sludge reactor lab scale anammox reactor. Results Differential coverage binning was assemble the genomes 17 new species, two which are proposed Candidatus genus. In addition, recovered first representative genome belonging genus ‘Ca. Villigracilis’. Even though samples analyzed were collected from bioreactors operating under environmental conditions, assembled share several features: anaerobic metabolism, fermentative pathways genes coding for hydrolytic enzymes. Interestingly, analysis indicated putative role nitrogen conversion. Genes related adhesiveness exopolysaccharides production also detected. Complementing sequencing analysis, filamentous morphology detected by Fluorescent situ hybridization. Conclusion Our results suggest participate organic matter degradation, removal biofilm aggregation, playing according conditions.

Language: Английский

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Single-cell approaches in human microbiome research

Cell, Journal Year: 2022, Volume and Issue: 185(15), P. 2725 - 2738

Published: July 1, 2022

Language: Английский

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Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: March 7, 2023

In terms of the number and diversity living units, prokaryotic empire is most represented form life on Earth, yet it still to a significant degree shrouded in darkness. This microbial “dark matter” hides great deal potential phylogenetically or metabolically diverse microorganisms, thus important acquire them pure culture. However, do we know what microorganisms really need for their growth, obstacles are cultivation previously unidentified taxa? Here review common sometimes unexpected requirements environmental especially soil-harbored bacteria, needed replication cultivation. These include resuscitation stimuli, physical chemical factors aiding cultivation, growth factors, co-cultivation laboratory natural neighborhood.

Language: Английский

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High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery

Metabolites, Journal Year: 2023, Volume and Issue: 13(5), P. 625 - 625

Published: May 2, 2023

Due to the continued emergence of resistance and a lack new promising antibiotics, bacterial infection has become major public threat. High-throughput screening (HTS) allows rapid large collection molecules for bioactivity testing holds promise in antibacterial drug discovery. More than 50% antibiotics that are currently available on market derived from natural products. However, with easily discoverable being found, finding sources seen limited success. Finding activity also proven be challenging. In addition exploring products synthetic biology, omics technology helped study biosynthetic machinery existing enabling construction unnatural synthesizers bioactive identification molecular targets agents. On other hand, newer smarter strategies have been continuously pursued screen molecule libraries druggable targets. Biomimetic conditions explored mimic real model better ligand–target interaction enable designing more effective drugs. This narrative review describes various traditional contemporaneous approaches high-throughput It further discusses critical factors HTS assay design, makes general recommendation, possible alternatives

Language: Английский

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Sequencing-based analysis of microbiomes

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: 25(12), P. 829 - 845

Published: June 25, 2024

Language: Английский

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Highly parallelized droplet cultivation and prioritization of antibiotic producers from natural microbial communities

eLife, Journal Year: 2021, Volume and Issue: 10

Published: March 25, 2021

Antibiotics from few culturable microorganisms have saved millions of lives since the 20th century. But with resistance formation, these compounds become increasingly ineffective, while majority microbial and that chemical compound diversity remains inaccessible for cultivation exploration. Culturing recalcitrant bacteria is a stochastic process. conventional methods are limited to low throughput. By increasing (i) throughput (ii) sensitivity by miniaturization, we innovate microbiological comply biological stochasticity. Here, introduce droplet-based microscale system, which directly coupled high-throughput screening antimicrobial activity prior strain isolation. We demonstrate highly parallelized in-droplet starting single cells results in yet uncultured species significantly higher bacterial than standard agar plate cultivation. Strains able inhibit intact reporter strains were isolated system. A variety detected selected potent antibiotic producer.

Language: Английский

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