The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes

Ma, Sierra; Bhattacharya, Chandrima; Ryon, K; Meierovich, S; Shaaban, Heba; Westfall, David A.; Mohammad, Rawhi; Kuchin, Katerina; Afshinnekoo, Ebrahim; Dc, Danko; Ce, Mason

doi:10.1101/2019.12.20.860569

Cited by 13 publications

(12 citation statements)

References 25 publications

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“…However, custom and up-to-date databases are encouraged in order to validate the veracity of taxonomic annotations, avoid misclassifications, and improve taxonomic assignation at lower taxonomic levels. Additionally, databases with validated taxonomy and phenotypic and ecological characterization of species found in the microbiome are essential to understanding the role of the microbes in the microbiome [52,53].…”

Section: Discussionmentioning

confidence: 99%

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Sierra

Pushalkar

et al. 2020

Genes

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There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

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Section: Discussionmentioning

confidence: 99%

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Sierra

Pushalkar

et al. 2020

Genes

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“…A cladogram of these species was built using the Environment for Tree Exploration (ETE) toolkit (40) and extremophile profile was incorporated using ggtree (98). To generate the extremophiles profile, the latest version (unpublished) of our database, The Microbe Directory (TMD) was used (78). The Microbe Directory is a database that contains morphological and ecologic characteristics of microbes and is based on published literature and manual curation (54).…”

Section: Methodsmentioning

confidence: 99%

Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

Sierra

Ryon

Tierney

et al. 2022

Preprint

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Background Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Our results are evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate a core microbiome in Lake Hillier composed of multiple pigment-producer microbes, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria and archaea, only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australias Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.

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“…We found and annotated genes on MAGs using Prodigal [32] and PROKKA [33]. Proteins associated with the following 5 categories were evaluated: DNA repair, chemotaxis, biocide resistance, sporulation, and antimicrobial resistance, using lists present in The Microbe Directory [34]. All categories are related to significant modes of microbial resistance against the extensive sanitization and other adverse conditions of the clean rooms environments.…”

Section: Characterization Of Magsmentioning

confidence: 99%

“…These properties, in turn, are often found in microbes which can form spores, biofilms, or that are found in extreme locations on earth. We annotated observed microbes for these features using The Microbe Directory [34]. The Microbe Directory includes annotations for species known to be radiophilic, psychrophilic, found in extreme environments, and to form spores or biofilms.…”

Section: Samples Include Taxa With Attributes Useful To Survive Spaceflightmentioning

confidence: 99%

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

et al. 2021

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Background Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Previous studies have attempted to characterize the microbial cargo through sequencing and culture-dependent protocols. However, there is not a standardized metagenomic workflow nor analysis pipeline for spaceflight hardware cleanroom samples to identify microbial contamination. Additionally, current identification methods fail to characterize and profile the risk of low-abundance microorganisms. Results A comprehensive metagenomic framework to characterize microorganisms relevant for planetary protection in multiple cleanroom classifications (from ISO-5 to ISO-8.5) and sample types (surface, filters, and debris collected via vacuum devices) was developed. Fifty-one metagenomic samples from SAF clean rooms were sequenced and analyzed to identify microbes that could potentially survive spaceflight based on their microbial features and whether the microbes expressed any metabolic activity or growth. Additionally, an auxiliary testing was performed to determine the repeatability of our techniques and validate our analyses. We find evidence that JPL clean rooms carry microbes with attributes that may be problematic in space missions for their documented ability to withstand extreme conditions, such as psychrophilia and ability to form biofilms, spore-forming capacity, radiation resistance, and desiccation resistance. Samples from ISO-5 standard had lower microbial diversity than those conforming to ISO-6 or higher filters but still carried a measurable microbial load. Conclusions Although the extensive cleaning processes limit the number of microbes capable of withstanding clean room condition, it is important to quantify thresholds and detect organisms that can inform ongoing Planetary Protection goals, provide a biological baseline for assembly facilities, and guide future mission planning.

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The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes

Cited by 13 publications

References 25 publications

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

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