A5003227888- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Anaerobic Digestion and Biogas Production
- Gut microbiota and health
- Plant Pathogenic Bacteria Studies
- Bacteriophages and microbial interactions
- Environmental DNA in Biodiversity Studies
- Probiotics and Fermented Foods
- Metabolomics and Mass Spectrometry Studies
- Legume Nitrogen Fixing Symbiosis
- Phytoplasmas and Hemiptera pathogens
- Plant-Microbe Interactions and Immunity
- Plant Virus Research Studies
- Fecal contamination and water quality
- Microbial bioremediation and biosurfactants
- Evolution and Genetic Dynamics
- Wastewater Treatment and Nitrogen Removal
- Antibiotic Resistance in Bacteria
- Water Treatment and Disinfection
- Protist diversity and phylogeny
- Cassava research and cyanide
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Methane Hydrates and Related Phenomena
Universität Innsbruck
2020-2025
Georgia Institute of Technology
2014-2024
Institut de Recherche pour le Développement
2013-2019
Université de Montpellier
2019
Centre de Coopération Internationale en Recherche Agronomique pour le Développement
2019
CNR de la Résistance aux Antibiotiques
2012-2014
Agropolis International
2012-2014
Laboratoire des Interactions Plantes Micro-Organismes
2014
Universidad de Los Andes
2009-2013
Institut de Recherche pour le Développement
2013
A fundamental question in microbiology is whether there continuum of genetic diversity among genomes, or clear species boundaries prevail instead. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) help address this by facilitating high resolution taxonomic analysis thousands genomes from diverse phylogenetic lineages. To scale to available and beyond, we present FastANI, a new method estimate ANI using alignment-free approximate sequence mapping. FastANI accurate for...
Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set actively maintained for tasks microbial genomics metagenomics, present graphical user interface case studies. Our resource includes previously described well new algorithms such Transformed-space Resampling In Biased Sets (TRIBS),...
Whether bacterial species exist as a natural unit remains an unresolved issue, one with important practical challenges, including that of correctly identifying microorganisms and diagnosing the causative agents microbial diseases. The current definition is based on genetic phenotypic distinctiveness organisms grouped under same name.
This study explored the short-term planktonic microbial community structure and resilience in Lake Lanier (GA, USA) while simultaneously evaluating technical aspects of identifying taxa via 16S rRNA gene amplicon metagenomic sequence data. amplicons generated from four temporally discrete samples were sequenced with 454 GS-FLX-Ti yielding ∼40,000 sequences each sample representing ∼300 observed OTUs. Replicates obtained same biological clustered together but several biases observed, linked...
Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across fields environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, homology-based bioinformatics framework to classify metagenomic genomic with unprecedented accuracy. The distinguishing aspect MyTaxa is it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power...
The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species communities but it offers limited resolution at finer levels, cannot represent whole-genome fluidity. To overcome these limitations, we introduced Microbial Genomes Atlas (MiGA), a webserver that allows classification an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well...
Genomic and metagenomic analyses are increasingly becoming commonplace in several areas of biological research, but recurrent specialized frequently reported as in-house scripts rarely available after publication. We describe the enveomics collection, a growing set actively maintained for tasks microbial genomics metagenomics, present graphical user interface case studies. Our resource includes previously described well new algorithms such Transformed-space Resampling In Biased Sets (TRIBS),...
The composition and prevalence of microorganisms in the middle-to-upper troposphere (8–15 km altitude) their role aerosol-cloud-precipitation interactions represent important, unresolved questions for biological atmospheric science. In particular, airborne above oceans remain essentially uncharacterized, as most work to date is restricted samples taken near Earth’s surface. Here we report on microbiome low- high-altitude air masses sampled onboard National Aeronautics Space Administration...
Abstract Motivation: Determining the fraction of diversity within a microbial community sampled and amount sequencing required to cover total represent challenging issues for metagenomics studies. Owing these limitations, central ecological questions with respect global distribution microbes functional their communities cannot be robustly assessed. Results: We introduce Nonpareil, method estimate project coverage in metagenomes. Nonpareil does not rely on high-quality assemblies, operational...
Estimations of microbial community diversity based on metagenomic data sets are affected, often to an unknown degree, by biases derived from insufficient coverage and reference database-dependent estimations diversity. For instance, the completeness databases cannot be generally estimated since it depends extant sampled date, which, with exception a few habitats such as human gut, remains severely undersampled. Further, estimation degree set is prohibitively time-consuming for large sets,...
Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata each sample, is still needed to identify the globally distributed community members serve as reliable repository.Here, 134 publicly available metagenomes derived from different were used recover 1635 metagenome-assembled genomes (MAGs) representing bacterial archaeal species. All estimated be > 50% complete...
A fundamental question in microbiology is whether there a continuum of genetic diversity among genomes or clear species boundaries prevail instead. Answering this requires robust measurement whole-genome relatedness thousands and from diverge phylogenetic lineages. Whole-genome similarity metrics such as Average Nucleotide Identity (ANI) can provide the resolution needed for task, overcoming several limitations traditional techniques used same purposes. Although number currently available...
Abstract Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules recommendations of International Code Nomenclature Prokaryotes (ICNP). Here we summarize development SeqCode, a code nomenclature which genome sequences serve nomenclatural types. This enables valid publication names based upon isolate genome, metagenome-assembled or single-amplified sequences. Otherwise, it is similar to ICNP with regard formation priority. It operates through...
Metagenome assembly and the recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental clinical settings. However, extent to which MAGs can capture genes population they represent remains speculative.
Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species has gone unnoticed so far could be used to more accurately precisely define these related compared current methods. These findings advance the molecular toolbox delineating following important units diversity within prokaryotic...
Abstract What a strain is and how many strains make up natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns assessed genomes against companion short-read metagenomes same samples. The distribution genome-aggregate average...
Microbial activities in soils, such as (incomplete) denitrification, represent major sources of nitrous oxide (N2O), a potent greenhouse gas. The key enzyme for mitigating N2O emissions is NosZ, which catalyzes reduction to N2. We recently described "atypical" functional NosZ proteins encoded by both denitrifiers and nondenitrifiers, were missed previous environmental surveys (R. A. Sanford et al., Proc. Natl. Acad. Sci. U. S. 109:19709-19714, 2012, doi:10.1073/pnas.1211238109). Here, we...
Soil microbial communities are extremely complex, being composed of thousands low-abundance species (<0.1% total). How such complex respond to natural or human-induced fluctuations, including major perturbations as global climate change, remains poorly understood, severely limiting our predictive ability for soil ecosystem functioning and resilience. In this study, we compared 12 whole-community shotgun metagenomic data sets from a grassland in the Midwestern United States, half representing...
ABSTRACT Although the source of drinking water (DW) used in hospitals is commonly disinfected, biofilms forming on pipelines are a refuge for bacteria, including possible pathogens that survive different disinfection strategies. These biofilm communities only beginning to be explored by culture-independent techniques circumvent limitations conventional monitoring efforts. Hence, theories regarding frequency opportunistic DW and how members withstand high doses disinfectants and/or chlorine...
Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, catalogue freshwater remains limited, most genome recovery attempts ecosystems only targeted specific taxa. Here, we present a pipeline incorporating iterative subtractive binning, apply it time series 100 metagenomic datasets seven connected lakes estuaries along Chattahoochee River (Southeastern USA)....