Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Nov. 22, 2023

Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify prevalence of amino acid auxotrophies across a broad diversity bacteria and habitats. We predicted biosynthetic capabilities 26,277 unique bacterial genomes spanning 12 phyla using metabolic pathway model validated with empirical data. Amino auxotrophy is widespread phyla, but conservatively estimate that majority taxa (78.4%) able all acids. Our estimates indicate more prevalent among obligate intracellular parasites in free-living genomic attributes characteristic 'streamlined' life history strategies. communities found habitats investigate environmental associations auxotrophy, data compiled from 3813 samples major aquatic, terrestrial, engineered environments. Auxotrophic were abundant host-associated environments (including human oral cavity gut) fermented food products, auxotrophic being relatively rare soil aquatic systems. Overall, work contributes complete understanding tree ecological contexts which can be successful strategy.

Language: Английский

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Isolation and Cultivation of Human Gut Microorganisms: A Review

Microorganisms, Journal Year: 2023, Volume and Issue: 11(4), P. 1080 - 1080

Published: April 20, 2023

Microbial resources from the human gut may find use in various applications, such as empirical research on microbiome, development of probiotic products, and bacteriotherapy. Due to “culturomics”, number pure bacterial cultures obtained has significantly increased since 2012. However, there is still a considerable microbes be isolated cultured. Thus, improve efficiency obtaining microbial gut, some constraints current methods, labor burden, culture condition, targetability, need optimized. Here, we overview general knowledge recent culturomics for microorganisms. Furthermore, discuss optimization several parts including sample collection, processing, isolation, cultivation, which strategies.

Language: Английский

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Advances in the isolation, cultivation, and identification of gut microbes

Military Medical Research, Journal Year: 2024, Volume and Issue: 11(1)

Published: June 3, 2024

Abstract The gut microbiome is closely associated with human health and the development of diseases. Isolating, characterizing, identifying microbes are crucial for research on essential advancing our understanding utilization it. Although culture-independent approaches have been developed, a pure culture required in-depth analysis disease mechanisms biotherapy strategies. Currently, faces challenge expanding existing database culturable microbiota rapidly isolating target microorganisms. This review examines advancements in microbe isolation cultivation techniques, such as culturomics, droplet microfluidics, phenotypic genomics selection, membrane diffusion. Furthermore, we evaluate progress made technology considering both non-targeted targeted focus future microbial culturomics expected to be high-throughput, automation, integration. Advancements this field may facilitate strain-level investigation into underlying diseases related microbiota.

Language: Английский

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Droplet microfluidic system for high throughput and passive selection of bacteria producing biosurfactants

Lab on a Chip, Journal Year: 2024, Volume and Issue: 24(7), P. 1947 - 1956

Published: Jan. 1, 2024

Novel microfluidic technique for functional selection of biosurfactant-producing microorganisms. Single bacterial cells are encapsulated into picoliter droplets clonal cultivation and passively sorted at high throughput by interfacial tension.

Language: Английский

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Modern microbiology: Embracing complexity through integration across scales

Cell, Journal Year: 2024, Volume and Issue: 187(19), P. 5151 - 5170

Published: Sept. 1, 2024

Language: Английский

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