Abstract:
:GapMind is a Web-based tool for annotating amino acid biosynthesis in bacteria and archaea (http://papers.genomics.lbl.gov/gaps). GapMind incorporates many variant pathways and 130 different reactions, and it analyzes a genome in just 15 s. To avoid error-prone transitive annotations, GapMind relies primarily on a database of experimentally characterized proteins. GapMind correctly handles fusion proteins and split proteins, which often cause errors for best-hit approaches. To improve GapMind's coverage, we examined genetic data from 35 bacteria that grow in defined media without amino acids, and we filled many gaps in amino acid biosynthesis pathways. For example, we identified additional genes for arginine synthesis with succinylated intermediates in Bacteroides thetaiotaomicron, and we propose that Dyella japonica synthesizes tyrosine from phenylalanine. Nevertheless, for many bacteria and archaea that grow in minimal media, genes for some steps still cannot be identified. To help interpret potential gaps, GapMind checks if they match known gaps in related microbes that can grow in minimal media. GapMind should aid the identification of microbial growth requirements.IMPORTANCE Many microbes can make all of the amino acids (the building blocks of proteins). In principle, we should be able to predict which amino acids a microbe can make, and which it requires as nutrients, by checking its genome sequence for all of the necessary genes. However, in practice, it is difficult to check for all of the alternative pathways. Furthermore, new pathways and enzymes are still being discovered. We built an automated tool, GapMind, to annotate amino acid biosynthesis in bacterial and archaeal genomes. We used GapMind to list gaps: cases where a microbe makes an amino acid but a complete pathway cannot be identified in its genome. We used these gaps, together with data from mutants, to identify new pathways and enzymes. However, for most bacteria and archaea, we still do not know how they can make all of the amino acids.
journal_name
mSystemsjournal_title
mSystemsauthors
Price MN,Deutschbauer AM,Arkin APdoi
10.1128/mSystems.00291-20subject
Has Abstractpub_date
2020-06-23 00:00:00issue
3issn
2379-5077pii
5/3/e00291-20journal_volume
5pub_type
杂志文章相关文献
mSystems文献大全abstract::Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral pr...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00158-18
更新日期:2018-12-18 00:00:00
abstract::Microbiology, like many areas of life science research, is increasingly data-intensive. As such, bioinformatics and data science skills have become essential to leverage microbiome sequencing data for discovery. Short intensive courses have sprung up as formal computational training opportunities at individual institu...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00467-19
更新日期:2019-08-20 00:00:00
abstract::For mammals, oxalate enters the body through the diet or is endogenously produced by the liver; it is removed by microbial oxalate metabolism in the gut and/or excretion in feces or urine. Deficiencies in any one of the these pathways can lead to complications, such as calcium oxalate urinary stones. While considerabl...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00088-17
更新日期:2017-09-26 00:00:00
abstract::Gut microbial β-glucuronidase (GUS) enzymes play important roles in drug efficacy and toxicity, intestinal carcinogenesis, and mammalian-microbial symbiosis. Recently, the first catalog of human gut GUS proteins was provided for the Human Microbiome Project stool sample database and revealed 279 unique GUS enzymes org...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00452-19
更新日期:2019-08-27 00:00:00
abstract::High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically ass...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00093-19
更新日期:2019-09-10 00:00:00
abstract::Quantitative understanding and prediction of microbial community dynamics are an outstanding challenge. We test the hypothesis that metabolic mechanisms provide a foundation for accurate prediction of dynamics in microbial systems. In our research, metabolic models have been able to accurately predict species interact...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00146-19
更新日期:2019-06-11 00:00:00
abstract::Polymyxins are a last-line therapy against multidrug-resistant Pseudomonas aeruginosa; however, resistance to polymyxins has been increasingly reported. Therefore, understanding the mechanisms of polymyxin activity and resistance is crucial for preserving their clinical usefulness. This study employed comparative meta...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00149-18
更新日期:2019-01-08 00:00:00
abstract::Biocathodes provide a stable electron source to drive reduction reactions in electrotrophic microbial electrochemical systems. Electroautotrophic biocathode communities may be more robust than monocultures in environmentally relevant settings, but some members are not easily cultivated outside the electrode environmen...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00002-17
更新日期:2017-03-28 00:00:00
abstract::Arctic regions, which are changing rapidly as they warm 2 to 3 times faster than the global average, still retain microbial habitats that serve as natural laboratories for understanding mechanisms of microbial adaptation to extreme conditions. Seawater-derived brines within both sea ice (sea-ice brine) and ancient lay...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00246-20
更新日期:2020-06-16 00:00:00
abstract::Classified as a biosafety level 4 (BSL4) select agent, Nipah virus (NiV) is a deadly henipavirus in the Paramyxoviridae family, with a nearly 75% mortality rate in humans, underscoring its global and animal health importance. Elucidating the process of viral particle production in host cells is imperative both for tar...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00194-19
更新日期:2019-09-24 00:00:00
abstract::Intestinal bacterial dysbiosis has been increasingly linked to ankylosing spondylitis (AS), which is a prototypic and best studied subtype of spondyloarthritis (SpA). Fungi and bacteria coexist in the human gut and interact with each other. Although they have been shown to contribute actively to health or disease, no ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00176-18
更新日期:2019-03-26 00:00:00
abstract::Insights into the interaction between phages and their bacterial hosts are crucial for the development of phage therapy. However, only one study has investigated global gene expression of Clostridioides (formerly Clostridium) difficile carrying prophage, and transcriptional reprogramming during lytic infection has not...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00017-20
更新日期:2020-05-05 00:00:00
abstract::ABSRTACTKlebsiella pneumoniae is a common cause of human-pneumonia-derived sepsis with high morbidity and mortality. The microbiota promotes and maintains host immune homeostasis. The mechanisms by which the gut microbiota affects the host defenses in the respiratory system systematically, however, remain poorly under...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00587-20
更新日期:2020-11-03 00:00:00
abstract::The intestinal microbiota contains trillions of commensal microorganisms that shape multiple aspects of host physiology and disease. In contrast to the host's genome, the microbiome is amenable to change over the course of an organism's lifetime, providing an opportunity to therapeutically modulate the microbiome's im...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00216-18
更新日期:2019-02-19 00:00:00
abstract::DNA methylation in prokaryotes is widespread. The most common modification of the genome is the methylation of adenine at the N-6 position. In Escherichia coli K-12 and many gammaproteobacteria, this modification is catalyzed by DNA adenine methyltransferase (Dam) at the GATC consensus sequence and is known to modulat...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00130-16
更新日期:2016-12-13 00:00:00
abstract::Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00668-20
更新日期:2020-08-25 00:00:00
abstract::Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic pot...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00125-20
更新日期:2020-06-02 00:00:00
abstract::Increasing rates of antibiotic-resistant bacterial infection are one of the most pressing contemporary global health concerns. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have been identified as the...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00024-18
更新日期:2018-04-17 00:00:00
abstract::Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00614-20
更新日期:2020-07-21 00:00:00
abstract::Networks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assemb...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00124-19
更新日期:2019-05-21 00:00:00
abstract::A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analy...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00534-20
更新日期:2020-10-06 00:00:00
abstract::Salmonella infection is one of the main causes of food-borne diarrheal diseases worldwide. Although most Salmonella infections can be cleared without treatment, some cause serious illnesses that require antibiotic treatment. In view of the growing emergence of antibiotic-resistant Salmonella strains, novel treatments ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00119-18
更新日期:2018-10-02 00:00:00
abstract::When organisms encounter an unfavorable environment, they transition to a physiologically distinct, quiescent state wherein abundant transcripts from the previous active growth state continue to persist, albeit their active transcription is downregulated. In order to generate proteins for the new quiescent physiologic...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00329-20
更新日期:2020-07-28 00:00:00
abstract::Trauma patients (TPs) are highly susceptible to infections, which often lead to sepsis. Among the numerous causative agents, Pseudomonas aeruginosa is especially important, as P. aeruginosa sepsis is often fatal. Understanding the mechanism of its pathogenesis in bloodstream infections is imperative; however, this mec...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00312-18
更新日期:2019-05-07 00:00:00
abstract::Apoptosis is generally considered the first line of defense against viral infection. However, the role of apoptosis in the interactions between plant viruses and their insect vectors has rarely been investigated. By studying plant DNA viruses of the genus Begomovirus within the family Geminiviridae, which are transmit...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00433-20
更新日期:2020-09-22 00:00:00
abstract::Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00057-17
更新日期:2017-08-22 00:00:00
abstract::Microbiome studies typically focus on characterizing the taxonomic and functional profiles of the microbes within a community. Functional profiling is generally thought to be superior to taxonomic profiling for investigating human-microbe interactions, but there are several limitations and challenges to existing appro...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00163-17
更新日期:2018-03-27 00:00:00
abstract::Although a few studies have investigated the intestinal microbiota of women with polycystic ovary syndrome (PCOS), the functional and metabolic mechanisms of the microbes associated with PCOS, as well as potential microbial biomarkers, have not yet been identified. To address this gap, we designed a two-phase experime...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00017-19
更新日期:2019-04-16 00:00:00
abstract::Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.00910-19
更新日期:2020-03-24 00:00:00
abstract::Pullorum disease is one of the most common diarrhea-related diseases caused by Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S Pullorum); it negatively affects the poultry industry. However, limited studies have explored the association between the gut microbiota and S Pullorum infection ...
journal_title:mSystems
pub_type: 杂志文章
doi:10.1128/mSystems.01192-20
更新日期:2021-01-05 00:00:00