Development of the Long Forms of Bacteria

Holman, R.A.

doi:10.1038/178424b0

Cited by 8 publications

(5 citation statements)

References 7 publications

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“…S6). Although this was unexpected, it has been observed that growing cells under microaerophilic or anaerobic conditions increases length ( 27 , 28 ).…”

Section: Resultsmentioning

confidence: 94%

“…As before, fermentative prokaryotes were more likely to be isolated from host-associated habitats, grow with shorter incubation time, and have longer cells. Thus, their long cells may owe partly to growth under anaerobic conditions ( 27 , 28 ), but it is not the full explanation. These results show that fermentative prokaryotes differ from anaerobic prokaryotes at large.…”

Section: Resultsmentioning

confidence: 99%

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The phenotype and genotype of fermentative prokaryotes

Hackmann,

Zhang

2023

Sci. Adv.

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Fermentation is a type of metabolism pervasive in oxygen-deprived environments. Despite its importance, we know little about the range and traits of organisms that carry out this metabolism. Our study addresses this gap with a comprehensive analysis of the phenotype and genotype of fermentative prokaryotes. We assembled a dataset with phenotypic records of 8350 organisms plus 4355 genomes and 13.6 million genes. Our analysis reveals fermentation is both widespread (in ~30% of prokaryotes) and complex (forming ~300 combinations of metabolites). Furthermore, it points to previously uncharacterized proteins involved in this metabolism. Previous studies suggest that metabolic pathways for fermentation are well understood, but metabolic models built in our study show gaps in our knowledge. This study demonstrates the complexity of fermentation while showing that there is still much to learn about this metabolism. All resources in our study can be explored by the scientific community with an online, interactive tool.

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“…S6). Although this was unexpected, it has been observed that growing cells under microaerophilic or anaerobic conditions increases length ( 27 , 28 ).…”

Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 99%

The phenotype and genotype of fermentative prokaryotes

Hackmann,

Zhang

2023

Sci. Adv.

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show abstract

“…5). Though this was surprising, it has been observed that growing cells under microaerophilic or anaerobic conditions increases length 31,32 .…”

Section: Resultsmentioning

confidence: 98%

“…5). Though this was surprising, it has been observed that growing cells under microaerophilic or anaerobic conditions increases length 31,32 . Though the differences were large, they were not as stark as they might be imagined to be.…”

Section: Fermentative Prokaryotes Have Distinct Phenotypic Traitsmentioning

confidence: 98%

“…As before, fermentative organisms were more likely to be isolated from host-associated habitats, grow with shorter incubation time, and have longer cells. Thus, their long cells may owe partly to growth under anaerobic conditions 31,32 , but it is not the full explanation. These results shows that fermentative organisms differ from anaerobic organisms at large.…”

Section: Fermentative Prokaryotes Have Distinct Phenotypic Traitsmentioning

confidence: 99%

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The phenotype and genotype of fermentative microbes

Hackmann

2023

Preprint

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Fermentation is a major type of metabolism carried out by many organisms. The study of this metabolism cuts across many fields, including cell biology, animal and human health, and biofuel production. Despite this broad importance, there has been no systematic study of fermentation across many organisms. Here we explore the phenotype and genotype of fermentative prokaryotes in order to gain insight into this metabolism. We assembled a dataset containing phenotypic records of 8,350 organisms (type strains) plus 4,355 genomes and 13.6 million genes. Fermentation was widespread, being found in 30% of all organisms and across the tree of life. Fermentative organisms were more likely than non-fermentative ones to have certain phenotypic traits. Some traits (such as oxygen insensitivity) were expected, but others (such as long cells) were surprising. Fermentative organisms also had a distinct genotype, with 9,450 gene functions and 337 metabolic pathways being more common in them. In a related analysis, we identified end products (metabolites) for 1,455 organisms fermenting 100 substrates. We found 55 products were formed in nearly 300 combinations, showing fermentation is more complex than previously realized. Additionally, we built metabolic models for 406 organisms and predicted which products they form. These models did not predict all products accurately, revealing gaps in our knowledge of metabolic pathways. Our study paints a full picture of fermentation while showing there is still much to learn about this type of metabolism. The microbiology community can explore resources in this work with an interactive tool (https://github.com/thackmann/FermentationExplorer).

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The biochemistry of carbon–halogen compounds

Doonan

1973

PATAI'S Chemistry of Functional Groups

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Development of the Long Forms of Bacteria

Cited by 8 publications

References 7 publications

The phenotype and genotype of fermentative prokaryotes

The phenotype and genotype of fermentative prokaryotes

The phenotype and genotype of fermentative microbes

The biochemistry of carbon–halogen compounds

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