Microbiome Laboratories

The Microbiome Laboratories (MGL) is a specialized research facility that provides advanced resources and expertise to support the analysis of microbial communities in various biological systems. This facility offers a range of services to researchers, including sample processing, NA extraction, preparation of sequencing library, and other molecular biological analyses (SNPs genotyping, gene expression analysis, ELISA analysis etc.).
Our core facility is staffed by expert molecular geneticists and microbiologists who work with researchers to design experiments that generate high-quality microbiome data. The facility's experts are proficient in a wide range of microbiome analysis techniques, including 16S and ITS rRNA gene sequencing, shotgun metagenomics, and target microbial species or gene analysis. The facility also provides support for sample collection and processing, including optimization of sampling protocols, and quality control checks.
The MGL core facility plays a critical role in advancing our understanding of the microbial communities that inhabit various ecosystems, including the human body, animals, models (organoids, biofilms), and environmental samples (soil, water, dust, etc.). By providing expert support and resources, this facility helps researchers to analyze microbiome data, identify microbial communities, and understand their roles in various biological systems. Ultimately, this work can lead to insights into the prevention and treatment of various diseases and improvements in environmental management practices.

Services

MGL provides state-of-the-art infrastructure, expert support, and service for a wide range of genomics applications to internal and external customers. This is a new core facility at the RECETOX Research Infrastructure primarily focuses on the analysis of microbial genome in the environmental, animal, and human samples, however, we are able to do also genomic analysis of human DNA and RNA. Our experienced experts use verified and standardized procedures for DNA isolation, qPCR analysis, and sequencing library preparation, including all necessary control steps. Our team works closely with specialists in biomedical bioinformatics and biostatisticians.
Our laboratories are fully equipped, we disposed with the molecular biological laboratories (laminar flow-boxes, thermocyclers, equipment for gel electrophoresis, UV-Vis spectrophotometers, imaging systems, centrifuges and others), as well as with the microbiological laboratory (incubator, microscope etc.). We have direct access to Real Time PCR systems at RECETOX; our lab collaborate with sequencing core facilities that have NGS technologies (Illumina NovaSeq equipment etc.), however, we can also use the massive parallel sequencers Illumina NextSeq and MiSeq equipment and Bioanalyzer or TapeStation at Masaryk University.

The Core facility is equipped with the following equipment and expertise:

Analysis and equipment

Analyses of microbiome

isolation of NA from microbial cultures, environmental, animal, and human samples
preparation of the library for 16S/ITS rRNA amplicon sequencing* for the bacteriome/mycobiome analysis in microbial DNA high/low-abundant matrices
preparation of the library for the sequencing analysis of bacterial/fungal cultures (whole genome sequencing, WGS)*
preparation of the library for Shotgun metagenomic sequencing (whole metagenome sequencing, WMGS)*
detection of DNA from selected oral and gut bacteria and their DNA quantification by qPCR method (single/multiplex qPCR analysis)
methodology development of a specific plex according to customer´s deman Analyses of human/animal genome/transcriptome/proteins
SNP genotyping by methods based on PCR
gene expression analysis by methods based on PCR
single/multiplex ELISA

* Note. The analyses result in FastQ files.

Consultations

Petra Bořilová Linhartová can provide you with consultations on the design experiment, analysis and interpretation of data, she will also provide you with the necessary information on the offered methods of analysis or consultation on planning the development of new methods.

Internships

Our researchers have extensive training experience in their respective fields of research. Trainings are tailored to the customer’s needs, however, are mainly focused on sample preparation, analysis, familiarization with laboratory technique and data interpretation. Training is done in the RECETOX laboratories.

Access

Access to the laboratories is available to academic users and researchers, including representatives of the commercial sphere and industry. Academic users and researchers can access through the Open Access project. Application for access available at: https://openaccess.recetox.cz/. Industrial users can directly contact coordinator of RECETOX Research Infrastructure RNDr. Petra Růžičková, Ph.D. (openaccess@recetox.muni.cz), who will answer questions about available capacities, expertise and other conditions of cooperation.

RECETOX Open Access system

Contact

For more information, please contact dr. Petra Bořilová Linhartová.

People

doc. RNDr. Petra Bořilová Linhartová, Ph.D., MBA

Head of Microbiome Laboratories and Environmental Genomics

Phone:	+420 775 393 703
E‑mail:
Web:	https://www.recetox.muni.cz/vyzkum/lide/doc-petra-borilova-linhartova

Mgr. Petra Brenerová, Ph.D.

Lab manager

Petra works at RECETOX RI as a laboratory manager, specializing in the analysis of the microbiome of the reproductive tract and the analysis of gene expression. She graduated in Biochemistry at the Faculty of Science MU, previously worked as a researcher at the Department of Pharmacology and Toxicology, Veterinary Research Institute in Brno. At the clinic of reproductive medicine in Brno, she gained experience in the field of Embryology and later worked as a manager of reproductive cell logistics around the world.

Mgr. Pavla Holochová, Ph.D.

Specialist

Pavla works at RECETOX RI as a specialist in molecular methods, specializing in the analysis of the microbiome in clinical samples, qPCR methodology, development of new methodologies and their implementation. She graduated in Molecular and Cell Biology at the Faculty of Science MU. Previously, she worked as a researcher and curator of the collection of microorganisms at the Czech Collection of Microorganisms, where she participated in the taxonomic identification of bacterial cultures using molecular methods, mainly by sequencing. For five years, she was employed as a consultant in the field of defeance against biological weapons for the Czech Army.

Mgr. Terezie Slámová

Administrator

Terezka works at RECETOX in an administrative position and is also involved in laboratory analyses of the microbiome and resistome. She is a Master's student of Biochemistry at the Faculty of Science, MU and her thesis is focused on the study of the resistome in hospitalized patients with inhalation trauma.

Mgr. Kateřina Navrátilová

Lab technician

Kačka works at RECETOX as a labratory technician in Microbiome laboratories. She is dealing with common laboratory work and is involved in microbiome analysis of clinical and enviromental samples as well as in qPCR analysis. She graduated in Molecular and Cell Biology at Palacký University in Olomouc, Faculty of Science. She gained laboratory experience by working at Institute of Experimental Botany of the Czech Academy of Sciences. She also gained her experience at the Faculty Hospital in Olomouc, namely at the Institute of Clinical and Molecular Pathology and then at the Institute of Medical Genetics.

Ing. Vojtěch Bartoň

Lab technician

Vojta works at RECETOX RI as a bioinformatician. He specializes in processing sequencing data. He is a graduate of the Biomedical Engineering and Bioinformatics program at Brno University of Technology, and is currently working on his doctoral thesis in the field of bioinformatics. In addition to data analysis, he is also engaged in developing new methods, teaching, and supervising students. He establishes and maintains pipelines for processing experiments and their evaluation. He maintains bioinformatics technology stack and ensures smooth analysis operations in a grid computing environment, guaranteeing results reproducibility.

Mgr. Jan Böhm

Lab technician

Honza is a biostatistician at RECETOX. He studied statistics and data analysis at the Faculty of Science, Masaryk University, and continues his doctoral studies at RECETOX. He is involved in projects from their very beginning, working on their design, and then at their end, evaluating the collected data, testing hypotheses, creating tables, figures, and reports.