MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

Ruiz-Pérez, Carlos A.; Conrad, Roth E.; Konstantinidis, Konstantinos T.

doi:10.1186/s12859-020-03940-5

Cited by 83 publications

(64 citation statements)

References 40 publications

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“…We therefore used protein sequences in our strategy. The genomes were annotated by using the RAST server, as it had the lowest percentage of unannotated proteins, despite giving a high percentage of hypothetical proteins 33 , which is standard in CPR, as high numbers of their metabolic pathways and biosynthetic capacities have not yet been determined 7 .…”

Section: Discussionmentioning

confidence: 99%

Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Maatouk

Ibrahim

Rolain

et al. 2021

Preprint

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Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new unique branch, thanks to the intensive application of metagenomics and advances of sequencing technologies. Despite their ultra-small size, reduced genome and metabolic pathways which mainly depend on symbiotic/exo-parasitic relationship with their bacterial host, CPR microbes are abundant and ubiquitous in almost all environments and are consequently survivors in highly competitive circumstances within microbial communities. They have been eventually identified by 16S rRNA analysis and represent more than 26% of microbial diversity. CPR microbes were able to survive in this context, although their defence mechanisms and phenotypic characteristic remain, however, poorly explored. Here, we conducted a thorough in-silico analysis on 4,062 CPR genomes to test whether these ultrasmall microorganisms might encode for antibiotic resistance (AR)-like enzymes. We used an adapted AR screening criteria with an exhaustive consensus database and complementary steps conferring their resistance functions. We conclude by reporting the surprising discovery of rich reservoir of divergent AR-like genes (n= 30,545 HITs, mean=7.5 HITs/genome [0-41] encoding for 89 AR enzymes, distributed across the 13 CPR phyla, and associated with 14 different chemical classes of antimicrobials. However, most HITs found (93.6%) were linked to glycopeptide, beta-lactams, macrolide-lincosamide-streptogramin, tetracycline and aminoglycoside resistance. Moreover, a distinct AR profile was discerned between the microgenomates group and Candidatus Parcubacteria, and between each of them and other CPR phyla. CPR cells seem to be active players during microbial competitive interactions and are well-equipped for the microbial combat in different habitats, supporting their natural survival/persistence and continued existence.

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Section: Discussionmentioning

confidence: 99%

Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Maatouk

Ibrahim

Rolain

et al. 2021

Preprint

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“…The percentages of each functional category were computed and plotted using pandas (Reback et al, 2020), seaborn and matplotlib (Reback et al, 2020). To assess the completeness of KEGG modules present in the pangenomes, MicrobeAnnotator was used in mode light (-light) with default options (Ruiz-Perez et al, 2021).…”

Section: Functional Annotation Of the Pangenomementioning

confidence: 99%

“…Additionally, KEGG annotations and assessment of pathways completeness were performed by MicrobeAnnotator (Ruiz-Perez et al, 2021). According to eggNOG-mapper, 32755 genes obtained any kind of functional annotation, i.e., COG, KEGG, GO or PFAM, of which 85.6% entries were assigned at least one COG category.…”

Section: Functional Annotation Of the Pangenomementioning

confidence: 99%

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

Maturana

Cárdenas

2021

Front. Microbiol.

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Blautia, a genus established in 2008, is a relevantly abundant taxonomic group present in the microbiome of human and other mammalian gastrointestinal (GI) tracts. Several described (or proposed) Blautia species are available at this date. However, despite the increasing level of knowledge about Blautia, its diversity is still poorly understood. The increasing availability of Blautia genomic sequences in the public databases opens the possibility to study this genus from a genomic perspective. Here we report the pangenome analysis and the phylogenomic study of 225 Blautia genomes available in RefSeq. We found 33 different potential species at the genomic level, 17 of them previously undescribed; we also confirmed by genomic standards the status of 4 previously proposed new Blautia species. Comparative genomic analyses suggest that the Blautia pangenome is open, with a relatively small core genome (∼ 700–800 gene families). Utilizing a set of representative genomes, we performed a gene family gain/loss model for the genus, showing that despite terminal nodes suffered more massive gene gain events than internal nodes (i.e., predicted ancestors), some ancestors were predicted to have gained an important number of gene families, some of them associated with the possible acquisition of metabolic abilities. Gene loss events remained lower than gain events in most cases. General aspects regarding pangenome composition and gene gain/loss events are discussed, as well as the proposition of changes in the taxonomic assignment of B. coccoidesTY and the proposition of a new species, “B. pseudococcoides.”

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“…Populations with no representative MAG having a MiGA quality score above 30% and/or redundancies below 5% were excluded from further analysis. Both Traitar 1.1.2 and MicrobeAnnotator were used with default settings to infer potential phenotypes and annotate draft genomes, respectively (46,47). Lastly, MAGs were screened for cross-reactivity using the FastANI tool to search for other genomes with ANI ≥ 95% across a suite of reference databases (48).…”

Section: Sample Collection Mesocosm Setup and Sample Processingmentioning

confidence: 99%

Novel municipal sewage-associated bacterial genomes and their potential in source tracking

Suttner

Conrad

et al. 2021

Preprint

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Little is known about the genomic diversity of raw municipal wastewater (sewage) microbial communities, including to what extent sewage-specific populations exist and how they can be used to improve source attribution and partitioning in sewage-contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) as inoculum in multiple controlled laboratory mesocosms to simulate sewage contamination events and followed these perturbed freshwater microbial communities with metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inoculum yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster under the well-aerated incubation conditions. Notably, a portion of these populations show decay patterns similar to common markers, Enterococcus and HF183. Comparisons against MAGs from different sources such as human and animal feces, revealed low cross-reactivity, indicating how genomic collections could be used to sensitively identify sewage contamination and partition signal among multiple sources. Overall, our results indicate the usefulness of metagenomic approaches for assessing sewage contamination in waterbodies and provides needed methodologies for doing so.

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MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes

Cited by 83 publications

References 40 publications

Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Small and equipped: the rich repertoire of antibiotic resistance genes in Candidate Phyla Radiation genomes

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

Novel municipal sewage-associated bacterial genomes and their potential in source tracking

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