A5063587965- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Climate change and permafrost
- Gut microbiota and health
- Polar Research and Ecology
- Probiotics and Fermented Foods
- Cryospheric studies and observations
- Environmental DNA in Biodiversity Studies
- Atmospheric and Environmental Gas Dynamics
- Meat and Animal Product Quality
- Plant Pathogens and Fungal Diseases
- Pharmaceutical and Antibiotic Environmental Impacts
- Peatlands and Wetlands Ecology
- Fermentation and Sensory Analysis
- Microbial Metabolism and Applications
- Composting and Vermicomposting Techniques
- Microbial bioremediation and biosurfactants
- Protist diversity and phylogeny
- Mycorrhizal Fungi and Plant Interactions
- Polyamine Metabolism and Applications
- Indoor Air Quality and Microbial Exposure
- Identification and Quantification in Food
- Antibiotic Resistance in Bacteria
- Gene expression and cancer classification
University of Helsinki
2016-2025
Natural Resources Institute Finland
2020-2025
University of Évora
2024
Finland University
2023
Ministère de la Santé et de l'Hygiène Publique
2020
Lawrence Berkeley National Laboratory
2010-2015
Pacific Northwest National Laboratory
2015
NASA Earth Science
2014
Helsinki Institute of Physics
2005
Abstract The Deepwater Horizon oil spill in the Gulf of Mexico resulted a deep-sea hydrocarbon plume that caused shift indigenous microbial community composition with unknown ecological consequences. Early history, bloom uncultured, thus uncharacterized, members Oceanospirillales was previously detected, but their role disposition unknown. Here our aim to determine functional and other active using deep sequencing DNA RNA, as well single-cell genomics. Shotgun metagenomic metatranscriptomic...
Abstract The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence exposure. Here we study potential sources ARGs by performing metagenomic sequencing breast milk, as well and maternal microbiomes. We find that fecal ARG mobile genetic element (MGE) profiles infants are more similar those their own mothers than unrelated mothers. MGEs mothers’ milk also shared with infants. Termination breastfeeding intrapartum prophylaxis...
Abstract Background Composting is an aerobic microbiological process that facilitated by bacteria and fungi. also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with efficiency biowaste degradation emission noxious odours. In this study we examine bacterial species richness community...
Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step process. By mixing large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots the emergence antibiotic resistant bacteria. Concerns have been expressed regarding to spread resistance genes (ARGs) environmental reservoirs human pathogens. We utilized epicPCR (Emulsion, Paired Isolation Concatenation PCR) detect bacterial hosts ARGs in two WWTPs. identified host...
Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity functions and activities
Chemolithotrophic ammonia-oxidising bacteria (AOB) present in oil-contaminated landfarming soil were studied over two growing seasons 1999 and 2000. The number of AOB (4-9 x 10(5) cellsg(-1) dry soil) determined with the quantitative polymerase chain reaction (real-time PCR) rate potential ammonium oxidation (0.05-0.28 microg NO2(-)-N g(-1) h(-1)) indicated presence stable populations. Denaturing gradient gel electrophoresis (DGGE) profiling sequence analysis PCR-amplified 16S rRNA genes...
One of the major environmental concerns Deepwater Horizon oil spill in Gulf Mexico was ecological impact that reached shorelines Coast. Here we investigated on microbial composition beach samples collected June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes community structure due to contamination were determined by deep sequencing 16S rRNA genes. Metatranscriptomics used determine expression functional genes involved hydrocarbon degradation...
ABSTRACT Refrigerated food processing facilities are specific man-made niches likely to harbor cold-tolerant bacteria. To characterize this type of microbiota and study the link between plant product microbiomes, we followed compared associated with raw materials stages a vacuum-packaged, cooked sausage affected by prolonged quality fluctuation occasional spoilage manifestations during shelf life. A total 195 samples were subjected culturing amplicon sequence analyses. Abundant mesophilic...
A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. provides a ontology dedicated classify functions relevant microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. 'profiles') were tailored large group target KEGG Orthologs (KOs) from which HMMs trained. The alignments checked and curated make them specific the targeted KO. Within this process,...
Microbial (colony counts, 16S rRNA gene amplification), chemical (pH, 1H NMR spectroscopy) and sensory changes in raw Atlantic Salmon (Salmo salar) tuna (Thunnus albacares) fillets stored under vacuum at 3 °C were evaluated over a period of 12 days. Both species fish are globally important among the ten most consumed fishes world. Although analyses showed decrease quality both species, only salmon considered spoiled end storage period. In salmon, trimethylamine was main spoilage product...
Low concentrations of antibiotics have numerous effects on bacteria. However, it is unknown whether ecological factors such as trophic interactions and spatial structuring influence the low multispecies microbial communities. Here, we address this question by investigating antibiotic concentration community composition horizontal transfer an resistance plasmid in a 62-strain bacterial response to manipulation environment presence predation. The strong treatment depend predation that their...
Summary A crucial step in the use of DNA markers for biodiversity surveys is assignment Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows all information known based on taxonomic names. Taxonomic placement barcoding sequences inherently probabilistic because contain errors, there natural variation among within a species, and reference data bases are incomplete can have false annotations. However, most existing bioinformatics methods either exclude uncertainty, or...
Abstract Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources greenhouse gas nitrous oxide (N 2 O). However, microorganisms involved in cycling N O this system remain largely uncharacterized. Since are variable and sinks O, we aimed at investigating differences community structure across different soil ecosystems tundra. Results We analysed 1.4 Tb metagenomic data from northern Finland covering a range dry upland...
Abstract Fungi are among the most diverse and ecologically important kingdoms in life. However, distributional ranges of fungi remain largely unknown as do ecological mechanisms that shape their distributions 1,2 . To provide an integrated view spatial seasonal dynamics fungi, we implemented a globally distributed standardized aerial sampling fungal spores 3 The vast majority operational taxonomic units were detected within only one climatic zone, spatiotemporal patterns species richness...
Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) present in numbers antibiotic-naive infants' gut microbiomes, infant mortality caused by resistant infections is high. The role antibiotics shaping the resistome has been studied, but there limited knowledge other factors that affect antibiotic burden gut.Our objectives were to determine impact early exposure formula ARG load neonates infants...
Novel methods for sampling and characterizing biodiversity hold great promise re-evaluating patterns of life across the planet. The airborne spores with a cyclone sampler, sequencing their DNA, have been suggested as an efficient well-calibrated tool surveying fungal diversity various environments. Here we present data originating from Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations world. Each sample represents DNA extracted 24 m
The microbiota at industrial full-scale composting plants has earlier been fragmentarily studied with molecular methods. Here, fungal communities from different stages of a and pilot-scale reactors were before after wood ash amendment.The portion biomass, determined using phospholipid fatty acid analysis, varied between 6.3% 38.5% in phases. internal transcribed spacer (ITS) area was cloned sequenced 19 samples representing the processes. Altogether 2986 clones grouped into 166 phylotypes...
Abstract Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them mobile and able to spread pathogenic bacteria. Until now, studying mobility antibiotic environmental resistomes has been challenging due inadequate sensitivity difficulties contig assembly metagenome based methods. We developed new cost labor efficient method on Inverse PCR long read sequencing for potential genes. applied sediment samples identified 79 different MGE clusters associated...
Water and sanitation are important factors in the emergence of antimicrobial resistance low- middle-income countries. Drug residues, metals, various wastes foster spread antibiotic genes (ARGs) with help mobile genetic elements (MGEs), therefore, rivers receiving contaminants effluents from multiple sources special interest. We followed both microbiome resistome Code River Indonesia its pristine origin at Merapi volcano through rural then city areas to coast Indian Ocean. used a SmartChip...