The phenotype and genotype of fermentative prokaryotes

Hackmann, Timothy J.; Zhang, Bo

doi:10.1126/sciadv.adg8687

Cited by 5 publications

(12 citation statements)

References 141 publications

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“…The simple definition of fermentation could be broadened to address some of these cases. It has been suggested the definition be broadened to include protons as an electron acceptor and H 2 as a second electron donor (Hackmann and Zhang 2023 ) (Table 1 ). The definition could likewise be broadened to include CO 2 as an electron acceptor.…”

Section: What Is Fermentation?mentioning

confidence: 99%

“…2 ). These studies examined descriptions of 8 300 prokaryotes, using both Bergey's Manual and the primary literature, and they found over 1/4 of these organisms carry out fermentation (Hackmann and Zhang 2021 , 2023 ). The definition of fermentation used in these studies is shown in Table 1 .…”

Section: Fermentative Organisms Are Diversementioning

confidence: 99%

“…Acetate and lactate are the most commonly formed products, but 55 end products are formed in all (Hackmann and Zhang 2023 ). Most organisms form multiple end products, and nearly 300 combinations are observed (Hackmann and Zhang 2023 ). Further, fermentation uses a range of substrates (Fig.…”

Section: Fermentative Organisms Are Diversementioning

confidence: 99%

“…glucose) into simpler ones (e.g. lactate) (Hackmann and Zhang 2023 ). This process releases adenosine triphosphate (ATP) without requiring oxygen.…”

Section: Introduction: Fermentation Allows Life To Thrive Without Oxygenmentioning

confidence: 99%

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The vast landscape of carbohydrate fermentation in prokaryotes

Hackmann

2024

FEMS Microbiology Reviews

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Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over ¼ of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.

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Section: What Is Fermentation?mentioning

confidence: 99%

Section: Fermentative Organisms Are Diversementioning

confidence: 99%

Section: Fermentative Organisms Are Diversementioning

confidence: 99%

“…glucose) into simpler ones (e.g. lactate) (Hackmann and Zhang 2023 ). This process releases adenosine triphosphate (ATP) without requiring oxygen.…”

Section: Introduction: Fermentation Allows Life To Thrive Without Oxygenmentioning

confidence: 99%

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The vast landscape of carbohydrate fermentation in prokaryotes

Hackmann

2024

FEMS Microbiology Reviews

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“…Aerobes, however, are different from anaerobes, and these differencesthough subtleare legible in their genomes. Aerobes tend to have larger genomes (4) with more O 2 utilizing enzymes (2,5) and usually belong to specific phylogenetic groups (4). Conversely, anaerobes make use of diverse fermentation pathways to conserve energy in low O 2 settings (3, 5).…”

Section: Introductionmentioning

confidence: 99%

Annotation-free prediction of microbial dioxygen utilization

Flamholz,

Goldford,

Larsson

et al. 2024

Preprint

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Aerobes require dioxygen (O2) to grow; anaerobes do not. But nearly all microbes — aerobes, anaerobes, and facultative organisms alike — express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes, encode more O2-utilizing enzymes, and tend to use different amino acids in their proteins. Here we show that these effects permit high-quality prediction of O2 utilization from genome sequences, with several models displaying >70% balanced accuracy on a ternary classification task wherein blind guessing is only 33.3% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genome sequence content — e.g. triplets of amino acids —perform about as well as intensive annotation-based algorithms, enabling the rapid processing of global-scale sequence data to predict aerobic physiology. To demonstrate the utility of efficient physiological predictions we estimated the prevalence of aerobes and anaerobes along a well-studied O2 gradient in the Black Sea, finding strong quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We therefore suggest that statistical methods like ours can be used to estimate, or “sense,” pivotal features of the environment from DNA sequencing data.

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Genomes OnLine Database (GOLD) v.10: new features and updates

Mukherjee,

Stamatis,

et al. 2024

Nucleic Acids Research

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The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

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The phenotype and genotype of fermentative prokaryotes

Cited by 5 publications

References 141 publications

The vast landscape of carbohydrate fermentation in prokaryotes

The vast landscape of carbohydrate fermentation in prokaryotes

Annotation-free prediction of microbial dioxygen utilization

Genomes OnLine Database (GOLD) v.10: new features and updates

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