Alla Lapidus
A5025927694- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Metal Extraction and Bioleaching
- Plant Pathogens and Fungal Diseases
- Probiotics and Fermented Foods
- Methane Hydrates and Related Phenomena
- RNA and protein synthesis mechanisms
- Mycotoxins in Agriculture and Food
- Legume Nitrogen Fixing Symbiosis
- Gut microbiota and health
- Biofuel production and bioconversion
- Molecular Biology Techniques and Applications
- Enzyme Production and Characterization
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- Plant-Microbe Interactions and Immunity
- Microbial Metabolism and Applications
- Mine drainage and remediation techniques
- Microbial Fuel Cells and Bioremediation
- Plant Pathogenic Bacteria Studies
- Microbial metabolism and enzyme function
- Plant Disease Resistance and Genetics
- Mycorrhizal Fungi and Plant Interactions
Independent University of Moscow
2024
Institute of Cytology
2024
St Petersburg University
2014-2023
Joint Genome Institute
2010-2020
Universidade de São Paulo
2020
RMIT University
2020
Research Institute of Influenza
2019
V.V. Dokuchaev Soil Science Institute
2019
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Bacillus subtilis is the best-characterized member of Gram-positive bacteria. Its genome 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these genes, 53% are represented once, while a quarter corresponds to several gene families that have been greatly expanded by duplication, largest family containing 77 putative ATP-binding transport proteins. In addition, large proportion genetic capacity devoted utilization variety carbon sources, including many plant-derived molecules. The...
SPAdes-St. Petersburg genome Assembler-was originally developed for de novo assembly of sequencing data produced cultivated microbial isolates and single-cell genomic DNA sequencing. With time, the functionality SPAdes was extended to enable IonTorrent data, as well hybrid from short long reads (PacBio Oxford Nanopore). In this article we present protocols five different pipelines that comprise package are used metagenomes transcriptomes putative plasmids biosynthetic gene clusters...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, assembly projects are challenging due (i) the highly nonuniform read coverage and (ii) a greatly elevated number chimeric reads pairs. While recently developed assemblers have addressed former challenge, methods for assembling remain poorly explored. We present algorithms identifying edges resolving complex bulges de...
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach taken the Genomic Encyclopedia of Bacteria Archaea (GEBA) project, advocates choosing organism's position, with aim filling gaps along branches tree life. value this demonstrated by pilot study genome sequences 56 culturable species selected maximize coverage. Analysis provides...
Following birth, the breast-fed infant gastrointestinal tract is rapidly colonized by a microbial consortium often dominated bifidobacteria. Accordingly, complete genome sequence of Bifidobacterium longum subsp. infantis ATCC15697 reflects competitive nutrient-utilization strategy targeting milk-borne molecules which lack nutritive value to neonate. Several chromosomal loci reflect potential adaptation host including 43 kbp cluster encoding catabolic genes, extracellular solute binding...
Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes1. It closely related to the animal and human anthracis insect thuringiensis, former being used as a biological weapon latter pesticide. B. thuringiensis are readily distinguished from presence of plasmid-borne specific toxins (B. thuringiensis) capsule anthracis). But phylogenetic studies based on analysis chromosomal genes bring controversial results, it unclear whether cereus,...
Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species colonize distinct trophic habitats in the oceans. Here, we compare genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic oligotrophic modes life specifically relate genomic features strategy these define their molecular mechanisms adaptation....
Abstract Background The possibility of generating large RNA-sequencing datasets has led to development various reference-based and de novo transcriptome assemblers with their own strengths limitations. While tools are widely used in transcriptomic studies, application is limited the organisms finished well-annotated genomes. De reconstruction from short reads remains an open challenging problem, which complicated by varying expression levels across different genes, alternative splicing,...
Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required fertility survival of human filarial parasitic nematode Brugia malayi. Although, quantitatively, even more degraded than those closely related Rickettsia species, Wolbachia has retained intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, nucleotides likely be Wolbachia's principal contribution mutualistic relationship,...
Comparative genomic analysis of “dry rot” fungus shows both convergent evolution and divergence among fungal decomposers.
Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and smallest known oxygenic phototroph. Numerous isolates from diverse areas of world's have been studied shown to be physiologically genetically distinct. All described thus far can assigned either tightly clustered high-light (HL)-adapted clade, or more divergent low-light (LL)-adapted group. The 16S rRNA sequences entire group differ by at most 3%, four initially published genomes revealed...
Recent fermentation studies have identified actinomycetes of the marine-dwelling genus Salinispora as prolific natural product producers. To further evaluate their biosynthetic potential, we sequenced 5,183,331-bp S. tropica CNB-440 circular genome and analyzed all identifiable secondary gene clusters. Our analysis shows that dedicates a large percentage its ( approximately 9.9%) to assembly, which is greater than previous Streptomyces sequences well other product-producing actinomycetes....
DNA from low-biodiversity fracture water collected at 2.8-kilometer depth in a South African gold mine was sequenced and assembled into single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, composes >99.9% of the microorganisms inhabiting fluid phase this particular fracture. Its genome indicates motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen carbon by using machinery shared with archaea. audaxviator is capable an...
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over past 2 years, (formerly EBI Metagenomics) has more than doubled number publicly available analysed datasets held within resource. Recently, an updated approach been unveiled (version 5.0), replacing previous single pipeline with multiple pipelines tailored...
Motivation: Plasmids are stably maintained extra-chromosomal genetic elements that replicate independently from the host cell’s chromosomes. Although plasmids harbor biomedically important genes, (such as genes involved in virulence and antibiotics resistance), there is a shortage of specialized software tools for extracting assembling plasmid data whole genome sequencing projects. Results: We present plasmidSPAdes algorithm tool benchmark its performance on diverse set bacterial genomes....
The lactic acid bacterium Streptococcus thermophilus is widely used for the manufacture of yogurt and cheese. This dairy species major economic importance phylogenetically close to pathogenic streptococci, raising possibility that it has a potential virulence. Here we report genome sequences two strains S. thermophilus. We found striking level gene decay (10% pseudogenes) in both microorganisms. Many genes involved carbon utilization are nonfunctional, line with paucity sources milk....
The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens humans, animals and crops, a source potent carcinogenic contaminants food, an genetic model. genome sequences eight aspergilli have already been explored investigate aspects biology, raising questions about evolution specialization within this genus.We generated for ten novel, highly diverse species compared these in detail sister more distant genera....
The complete genomic sequence of Pseudomonas syringae pv. B728a ( Pss B728a) has been determined and is compared with that P. tomato DC3000 Pst DC3000). two pathovars this economically important species plant pathogenic bacteria differ in host range other interactions plants, having a more pronounced epiphytic stage growth higher abiotic stress tolerance apoplastic habitat. genome (6.1 Mb) contains circular chromosome no plasmid, whereas the 6.5 mbp size, composed plasmids. Although high...
More detailed sequence standards that keep up with revolutionary sequencing technologies will aid the research community in evaluating data.
ABSTRACT Phytoplasmas (“ Candidatus Phytoplasma,” class Mollicutes ) cause disease in hundreds of economically important plants and are obligately transmitted by sap-feeding insects the order Hemiptera, mainly leafhoppers psyllids. The 706,569-bp chromosome four plasmids aster yellows phytoplasma strain witches' broom (AY-WB) were sequenced compared to onion M (OY-M) genome. phytoplasmas have small repeat-rich genomes. This comparative analysis revealed that repeated DNAs organized into...
Agaricus bisporus is the model fungus for adaptation, persistence, and growth in humic-rich leaf-litter environment. Aside from its ecological role, A. has been an important component of human diet over 200 y worldwide cultivation "button mushroom" forms a multibillion dollar industry. We present two genomes, their gene repertoires transcript profiles on compost during mushroom formation. The genomes encode full repertoire polysaccharide-degrading enzymes similar to that wood-decayers....
Abstract Background Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species closely related well studied model organism subtilis , produces an assortment of extracellular enzymes may contribute nutrient cycling nature. Results We determined complete nucleotide sequence B. ATCC 14580 genome which comprises circular chromosome 4,222,336 base-pairs (bp)...