Publications by authors named "Tomáš Větrovský"

46 Publications

Punch Trackers: Correct Recognition Depends on Punch Type and Training Experience.

Sensors (Basel) 2021 Apr 23;21(9). Epub 2021 Apr 23.

Faculty of Physical Education and Sport, Charles University, 16252 Prague, Czech Republic.

To determine the ability of different punch trackers (PT) (Corner (CPT), Everlast (EPT), and Hykso (HPT)) to recognize specific punch types (lead and rear straight punches, lead and rear hooks, and lead and rear uppercuts) thrown by trained (TR, n = 10) and untrained punchers (UNTR, n = 11), subjects performed different punch combinations, and PT data were compared to data from video recordings to determine how well each PT recognized the punches that were actually thrown. Descriptive statistics and multilevel modelling were used to analyze the data. The CPT, EPT and HPT detected punches more accurately in TR than UNTR, evidenced by a lower percentage error in TR ( = 0.007). The CPT, EPT, and HPT detected straight punches better than uppercuts and hooks, with a lower percentage error for straight punches ( < 0.001). The recognition of punches with CPT and HPT depended on punch order, with earlier punches in a sequence recognized better. The same may or may not have occurred with EPT, but EPT does not allow for data to be exported, meaning the order of individual punches could not be analyzed. The CPT and HPT both seem to be viable options for tracking punch count and punch type in TR and UNTR.
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http://dx.doi.org/10.3390/s21092968DOI Listing
April 2021

Benefits of Resistance Training in Early and Late Stages of Frailty and Sarcopenia: A Systematic Review and Meta-Analysis of Randomized Controlled Studies.

J Clin Med 2021 Apr 12;10(8). Epub 2021 Apr 12.

Human Performance and Sports Science Laboratory, Faculty of Sport Sciences, University of Murcia, 30730 Murcia, Spain.

Sarcopenia and frailty are age-related syndromes with negative effects on the quality of life of older people and on public health costs. Although extensive research has been carried out on the effects of physical exercise and physical syndromes, there is a knowledge gap when it comes to the effect of resistance training on muscular strength, physical performance, and body composition at early (prevention) and late (treatment) stages in both syndromes combined. We conducted this systematic review and meta-analysis (CRD42019138253) to gather the evidence of randomized controlled trials examining the effects of resistance training programs lasting ≥8 weeks on strength, physical function, and body composition of adults ≥65 years old diagnosed with pre-sarcopenia, sarcopenia, pre-frailty, or frailty. A search from the earliest record up to and including December 2020 was carried out using the PubMed, Scopus, Web of Science, and Cochrane Library databases. A total of 25 studies ( = 2267 participants) were included. Meta-analysis showed significant changes in favour of resistance training for handgrip (ES = 0.51, = 0.001) and lower-limb strength (ES = 0.93, < 0.001), agility (ES = 0.78, = 0.003), gait speed (ES = 0.75, < 0.001), postural stability (ES = 0.68, = 0.007), functional performance (ES = 0.76, < 0.001), fat mass (ES = 0.41, = 0.001), and muscle mass (ES = 0.29, = 0.002). Resistance training during early stages had positive effects in all variables during early stages (ES > 0.12), being particularly effective in improving gait speed (ES = 0.63, = 0.016) and functional strength (ES = 0.53, = 0.011). Based on these results, resistance training should be considered as a highly effective preventive strategy to delay and attenuate the negative effects of sarcopenia and frailty in both early and late stages.
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http://dx.doi.org/10.3390/jcm10081630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070531PMC
April 2021

Increased Cardiopulmonary Fitness Is Associated with a Greater Reduction in Depression among People Who Underwent Bariatric Surgery.

Int J Environ Res Public Health 2021 03 3;18(5). Epub 2021 Mar 3.

Human Performance and Sports Science Laboratory, Faculty of Sport Sciences, University of Murcia, 30720 Murcia, Spain.

The aim of this study was to determine the effect of changes in cardiopulmonary fitness on the mental health of patients with severe obesity who underwent gastric bypass surgery (prior to and 1, 3, and 6 months after surgery). Study participants were recruited from among patients of a regional hospital in Czechia who underwent gastric bypass surgery between April 2018 and October 2019. They were eligible if they (a) were between 18 and 65 years old, (b) provided written informed consent, and (c) were able to walk independently. Twenty-six patients (age 45.4 ± 9.0 years, body mass index 45.1 ± 7.4 kg·m, body fat 43.8 ± 4.8%) were included in the analysis. The key finding revealed that the greater the increase in cardiopulmonary fitness (i.e., longer distance walked in the six-minute walk test, 6MWT), the better the improvement in depression score among patients who underwent bariatric surgery. In particular, increments of 10 m in the 6MWT lead to the improvement of 0.5 points on the depression subscale of the Hospital Anxiety and Depression Scale (HADS) questionnaire. As the main implication, these results suggest that patients should participate in exercise training programs to increase their fitness status for optimal physical and mental outcomes of bariatric surgery.
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http://dx.doi.org/10.3390/ijerph18052508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7967516PMC
March 2021

R/G Value-A Numeric Index of Individual Periodontal Health and Oral Microbiome Dynamics.

Front Cell Infect Microbiol 2021 10;11:602643. Epub 2021 Mar 10.

Institute of Microbiology v. v. i., Czech Academy of Sciences, Prague, Czechia.

The dysbiosis of oral microbiome (OM) precedes the clinical signs of periodontal disease. Its simple measure thus could indicate individuals at risk of periodontitis development; however, such a tool is still missing. Up to now, numerous microbial taxa were associated with periodontal health or periodontitis. The outputs of most studies could, nevertheless, be slightly biased from following two reasons: First, the healthy group is often characterized only by the absence of the disease, but the individuals could already suffer from dysbiosis without any visible signs. Second, the healthy/diseased OM characteristics are frequently determined based on average data obtained for whole groups of periodontally healthy persons patients. Especially in smaller sets of tested individuals the typical individual variability can thus complicate the unambiguous assignment of oral taxa to respective state of health. In this work the taxonomic composition of OM was evaluated for 20 periodontally healthy individuals and 15 patients with chronic periodontitis. The narrowed selection set of the most diseased patients (confirmed by clinical parameters) and the most distant group of healthy individuals with the lowest probability of dysbiosis was determined by clustering analysis and used for identification of marker taxa. Based on their representation in each individual oral cavity we proposed the numeric index of periodontal health called R/G value. Its diagnostic potential was further confirmed using independent set of 20 periodontally healthy individuals and 20 patients with periodontitis with 95 percent of samples assigned correctly. We also assessed the individual temporal OM dynamics in periodontal health and we compared it to periodontitis. We revealed that the taxonomic composition of the system changes dynamically but generally it ranges within values typical for periodontal health or transient state, but far from values typical for periodontitis. R/G value tool, formulated from individually evaluated data, allowed us to arrange individual OMs into a continuous series, instead of two distinct groups, thus mimicking the gradual transformation of a virtual person from periodontal health to disease. The application of R/G value index thus represents a very promising diagnostic tool for early prediction of persons at risk of developing periodontal disease.
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http://dx.doi.org/10.3389/fcimb.2021.602643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7988090PMC
March 2021

Morning fatigue and structured exercise interact to affect non-exercise physical activity of fit and healthy older adults.

BMC Geriatr 2021 03 12;21(1):179. Epub 2021 Mar 12.

Department of Physiology and Biochemistry, Faculty of Physical Education and Sport, Charles University, Prague, Jose Martiho 269/31, 162 52, Prague, Czech Republic.

Background: Exercise training is crucial for maintaining physical and mental health in aging populations. However, as people participate in structured exercise training, they tend to behaviorally compensate by decreasing their non-exercise physical activity, thus potentially blunting the benefits of the training program. Furthermore, physical activity of older adults is substantially influenced by physical feelings such as fatigue. Nevertheless, how older people react to day-to-day fluctuations of fatigue and whether fatigue plays a role in non-exercise physical activity compensation is not known. Thus, the purpose of this study was twofold: (1) To explore whether the volume and intensity of habitual physical activity in older adults were affected by morning fatigue. (2) To investigate the effect of attending power and resistance exercise sessions on the levels of non-exercise physical activity later that day and the following day.

Methods: Twenty-eight older adults wore an accelerometer during a 4-week low-volume, low-intensity resistance and power training program with three exercise sessions per week and for 3 weeks preceding and 1 week following the program. During the same period, the participants were prompted every morning, using text messages, to rate their momentary fatigue on a scale from 0 to 10.

Results: Greater morning fatigue was associated with lower volume (p = 0.002) and intensity (p = 0.017) of daily physical activity. Specifically, one point greater on the fatigue scale was associated with 3.2 min (SE 1.0) less moderate-to-vigorous physical activity. Furthermore, attending an exercise session was associated with less moderate-to-vigorous physical activity later that day by 3.7 min (SE 1.9, p = 0.049) compared to days without an exercise session. During the next day, the volume of physical activity was greater, but only in participants with a body mass index up to 23 (p = 0.008).

Conclusions: Following low-volume exercise sessions, fit and healthy older adults decreased their non-exercise physical activity later that day, but this compensation did not carry over into the next day. As momentary morning fatigue negatively affects daily physical activity, we suggest that the state level of fatigue should be monitored during intensive exercise programs, especially in less fit older adults with increased fatigability.
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http://dx.doi.org/10.1186/s12877-021-02131-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953813PMC
March 2021

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.

mSystems 2021 Jan 12;6(1). Epub 2021 Jan 12.

Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic

Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils. Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.
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http://dx.doi.org/10.1128/mSystems.01078-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901482PMC
January 2021

Fungal Communities Are Important Determinants of Bacterial Community Composition in Deadwood.

mSystems 2021 Jan 5;6(1). Epub 2021 Jan 5.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.

Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood's properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
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http://dx.doi.org/10.1128/mSystems.01017-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7786133PMC
January 2021

Termites Are Associated with External Species-Specific Bacterial Communities.

Appl Environ Microbiol 2021 01 4;87(2). Epub 2021 Jan 4.

Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic

All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to and , which were often shared by several termite species. The abundance of several bacterial OTUs, such as , , , and , was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities. As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on and abundance and negative effects on the abundance of several ubiquitous genera, such as , , , and Our results demonstrate that termite galleries harbor unique bacterial communities.
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http://dx.doi.org/10.1128/AEM.02042-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783351PMC
January 2021

Overspeed Stimulus Provided by Assisted Jumping Encourages Rapid Increases in Strength and Power Performance of Older Adults.

J Aging Phys Act 2020 Sep 12;29(2):259-266. Epub 2020 Sep 12.

Following a 4-week control period, 24 older men and women (55-91 years) attended a 4-week progressive jumping program to determine whether assisted jumping could be safely and effectively implemented as a novel stimulus in healthy older adults. Bodyweight countermovement jump performance, isometric and isokinetic strength, postural stability, and exercise enjoyment were assessed before the control period, before the training intervention, and after the training intervention. Following the 4-week intervention, eccentric quadriceps strength increased by 19 N·m (95% confidence interval [2, 36], p = .013), bodyweight countermovement jump height increased by 1.7 cm (95% CI [0.5, 2.9], p < .001), postural sway improved by 2.1 mm/s (95% CI [0.3, 4.0], p = .026), and the participants' perceived exercise enjoyment improved (p = .026). Therefore, using assisted jumping to induce an overspeed training stimulus in a jump training program resulted in similar performance improvements as in previous studies in older populations but with less training volume and a shorter training duration.
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http://dx.doi.org/10.1123/japa.2020-0012DOI Listing
September 2020

Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass.

Environ Microbiol 2020 11 31;22(11):4604-4619. Epub 2020 Aug 31.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic.

Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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http://dx.doi.org/10.1111/1462-2920.15183DOI Listing
November 2020

The detrimental effect of COVID-19 nationwide quarantine on accelerometer-assessed physical activity of heart failure patients.

ESC Heart Fail 2020 10 22;7(5):2093-2097. Epub 2020 Jul 22.

2nd Department of Medicine-Department of Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.

Aims: A reduction of habitual physical activity due to prolonged COVID-19 quarantine can have serious consequences for patients with cardiovascular diseases, such as heart failure. This study aimed to explore the effect of COVID-19 nationwide quarantine on accelerometer-assessed physical activity of heart failure patients.

Methods And Results: We analysed the daily number of steps in 26 heart failure patients during a 6-week period that included 3 weeks immediately preceding the onset of the quarantine and the first 3 weeks of the quarantine. The daily number of steps was assessed using a wrist-worn accelerometer worn by the patients as part of an ongoing randomized controlled trial. Multilevel modelling was used to explore the effect of the quarantine on the daily step count adjusted for weather conditions. As compared with the 3 weeks before the onset of the quarantine, the step count was significantly lower during each of the first 3 weeks of the quarantine (P < 0.05). When the daily step count was averaged across the 3 weeks before and during the quarantine, the decrease amounted to 1134 (SE 189) steps per day (P < 0.001), which translated to a 16.2% decrease.

Conclusions: The introduction of the nationwide quarantine due to COVID-19 had a detrimental effect on the level of habitual physical activity in heart failure patients, leading to an abrupt decrease of daily step count that lasted for at least the 3-week study period. Staying active and maintaining sufficient levels of physical activity during the COVID-19 pandemic are essential despite the unfavourable circumstances of quarantine.
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http://dx.doi.org/10.1002/ehf2.12916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405478PMC
October 2020

GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies.

Sci Data 2020 07 13;7(1):228. Epub 2020 Jul 13.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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http://dx.doi.org/10.1038/s41597-020-0567-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359306PMC
July 2020

Assisted Jumping in Healthy Older Adults: Optimizing High-Velocity Training Prescription.

J Strength Cond Res 2020 Jul 7. Epub 2020 Jul 7.

Faculty of Physical Education and Sport, Charles University in Prague, Prague, Czech Republic.

Tufano, JJ, Vetrovsky, T, Stastny, P, Steffl, M, Malecek, J, and Omcirk, D. Assisted jumping in healthy older adults: optimizing high-velocity training prescription. J Strength Cond Res XX(X): 000-000, 2020-Because older adults benefit from power training, training strategies for athletes such as supramaximal velocity-assisted jumping could also be useful for older adults. However, optimizing-assisted exercise prescription in older adults remains uninvestigated. Therefore, the purpose of this study was to determine the effects of different bodyweight (BW) assistance levels on jumping force and velocity in healthy older adults. Twenty-three healthy older adults (67.6 ± 7.6 years, 167.0 ± 8.8 cm, 72.7 ± 14.3 kg, and 27.1 ± 6.9% body fat) performed 5 individual countermovement jumps at BW, 90, 80, 70, and 60% of BW. Jumps were performed on a force plate, which provided peak take-off force (TOF), flight time, and peak impact force. A linear position transducer measured peak concentric velocity (PV). The rating of perceived exertion (RPE) was also assessed after each condition. Take-off force was greater during BW than all other conditions, 90 and 80% were greater than 70 and 60%, but there were no differences between 80 and 90% or between 70 and 60%. The FT progressively increased at all assistance levels, and PV was faster for all assistance levels than BW, with no differences between assistance levels. Impact force was greater during BW than 80, 70, and 60% and was greater during 90% than 60%. The RPE was less than BW during all assistance conditions but was the least during 70%. Implementing assisted jumping between 70 and 80% of BW in older adults likely provides the ideal combination of force, velocity, and RPE.
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http://dx.doi.org/10.1519/JSC.0000000000003661DOI Listing
July 2020

Advances in accelerometry for cardiovascular patients: a systematic review with practical recommendations.

ESC Heart Fail 2020 10 3;7(5):2021-2031. Epub 2020 Jul 3.

2nd Department of Medicine-Department of Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.

Aims: Accelerometers are becoming increasingly commonplace for assessing physical activity; however, their use in patients with cardiovascular diseases is relatively substandard. We aimed to systematically review the methods used for collecting and processing accelerometer data in cardiology, using the example of heart failure, and to provide practical recommendations on how to improve objective physical activity assessment in patients with cardiovascular diseases by using accelerometers.

Methods And Results: Four electronic databases were searched up to September 2019 for observational, interventional, and validation studies using accelerometers to assess physical activity in patients with heart failure. Study and population characteristics, details of accelerometry data collection and processing, and description of physical activity metrics were extracted from the eligible studies and synthesized. To assess the quality and completeness of accelerometer reporting, the studies were scored using 12 items on data collection and processing, such as the placement of accelerometer, days of data collected, and criteria for non-wear of the accelerometer. In 60 eligible studies with 3500 patients (of those, 536 were heart failure with preserved ejection fraction patients), a wide variety of accelerometer brands (n = 27) and models (n = 46) were used, with Actigraph being the most frequent (n = 12), followed by Fitbit (n = 5). The accelerometer was usually worn on the hip (n = 32), and the most prevalent wear period was 7 days (n = 22). The median wear time required for a valid day was 600 min, and between two and five valid days was required for a patient to be included in the analysis. The most common measures of physical activity were steps (n = 20), activity counts (n = 15), and time spent in moderate-to-vigorous physical activity (n = 14). Only three studies validated accelerometers in a heart failure population, showing that their accuracy deteriorates at slower speeds. Studies failed to report between one and six (median 4) of the 12 scored items, with non-wear time criteria and valid day definition being the most underreported items.

Conclusions: The use of accelerometers in cardiology lacks consistency and reporting on data collection, and processing methods need to be improved. Furthermore, calculating metrics based on raw acceleration and machine learning techniques is lacking, opening the opportunity for future exploration. Therefore, we encourage researchers and clinicians to improve the quality and transparency of data collection and processing by following our proposed practical recommendations for using accelerometers in patients with cardiovascular diseases, which are outlined in the article.
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http://dx.doi.org/10.1002/ehf2.12781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7524133PMC
October 2020

Alien ectomycorrhizal plants differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in novel sites.

ISME J 2020 09 4;14(9):2336-2346. Epub 2020 Jun 4.

Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic.

Alien plants represent a potential threat to environment and society. Understanding the process of alien plants naturalization is therefore of primary importance. In alien plants, successful establishment can be constrained by the absence of suitable fungal partners. Here, we used 42 independent datasets of ectomycorrhizal fungal (EcMF) communities associated with alien Pinaceae and Eucalyptus spp., as the most commonly introduced tree species worldwide, to explore the strategies these plant groups utilize to establish symbioses with EcMF in the areas of introduction. We have also determined the differences in composition of EcMF communities associated with alien ectomycorrhizal plants in different regions. While alien Pinaceae introduced to new regions rely upon association with co-introduced EcMF, alien Eucalyptus often form novel interactions with EcMF species native to the region where the plant was introduced. The region of origin primarily determines species composition of EcMF communities associated with alien Pinaceae in new areas, which may largely affect invasion potential of the alien plants. Our study shows that alien ectomycorrhizal plants largely differ in their ability to interact with co-introduced and native ectomycorrhizal fungi in sites of introduction, which may potentially affect their invasive potential.
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http://dx.doi.org/10.1038/s41396-020-0692-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608243PMC
September 2020

Early successional ectomycorrhizal fungi are more likely to naturalize outside their native range than other ectomycorrhizal fungi.

New Phytol 2020 09 18;227(5):1289-1293. Epub 2020 Apr 18.

Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-142 20, Prague, Czech Republic.

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http://dx.doi.org/10.1111/nph.16557DOI Listing
September 2020

A meta-analysis of global fungal distribution reveals climate-driven patterns.

Nat Commun 2019 11 13;10(1):5142. Epub 2019 Nov 13.

Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.

The evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.
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http://dx.doi.org/10.1038/s41467-019-13164-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853883PMC
November 2019

Validity of six consumer-level activity monitors for measuring steps in patients with chronic heart failure.

PLoS One 2019 13;14(9):e0222569. Epub 2019 Sep 13.

2nd Department of Medicine - Department of Cardiovascular Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.

Introduction: Although numerous activity trackers have been validated in healthy populations, validation is lacking in chronic heart failure patients who normally walk at a slower pace, making it difficult for researchers and clinicians to implement activity monitors during physical activity interventions.

Methods: Six consumer-level activity monitors were validated in a 3-day field study in patients with chronic heart failure and healthy individuals under free living conditions. Furthermore, the same devices were evaluated in a lab-based study during treadmill walking at speeds of 2.4, 3.0, 3.6, and 4.2 km·h-1. Concordance correlation coefficients (CCC) were used to evaluate the agreement between the activity monitors and the criterion, and mean absolute percentage errors (MAPE) were calculated to assess differences between each device and the criterion (MAPE <10% was considered as a threshold for validity).

Results: In the field study of healthy individuals, all but one of the activity monitors showed a substantial correlation (CCC ≥0.95) with the criterion device and MAPE <10%. In patients with heart failure, the correlation of only two activity monitors (Garmin vívofit 3 and Withings Go) was classified as at least moderate (CCC ≥0.90) and none of the devices had MAPE <10%. In the lab-based study at speeds 4.2 and 3.6 km·h-1, all activity monitors showed substantial to almost perfect correlations (CCC ≥0.95) with the criterion and MAPE in the range 1%-3%. However, at slower speeds of 3.0 and 2.4 km·h-1, the accuracy of all devices substantially deteriorated: their correlation with the criterion decreased below 90% and their MAPE increased to 4-8% and 10-45%, respectively.

Conclusions: Even though none of the tested activity monitors fall within arbitrary thresholds for validity, most of them perform reasonably well enough to be useful tools that clinicians can use to simply motivate chronic heart failure patients to walk more.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222569PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6743766PMC
March 2020

Health Benefits of β-Hydroxy-β-Methylbutyrate (HMB) Supplementation in Addition to Physical Exercise in Older Adults: A Systematic Review with Meta-Analysis.

Nutrients 2019 Sep 3;11(9). Epub 2019 Sep 3.

Faculty of Physical Education and Sport, Charles University, Prague 16252, Czech Republic.

Both regular exercise training and beta-hydroxy-beta-methylbutyrate (HMB) supplementation are shown as effective treatments to delay or reverse frailty and reduce cognitive impairment in older people. However, there is very little evidence on the true benefits of combining both strategies. The aim of this meta-analysis was to quantify the effects of exercise in addition to HMB supplementation, on physical and cognitive health in older adults. Data from 10 randomized controlled trials (RCTs) investigating the effect of HMB supplementation and physical function in adults aged 50 years or older were analyzed, involving 384 participants. Results showed that HMB supplementation in addition to physical exercise has no or fairly low impact in improving body composition, muscle strength, or physical performance in adults aged 50 to 80 years, compared to exercise alone. There is a gap of knowledge on the beneficial effects of HMB combined with exercise to preserve cognitive functions in aging and age-related neurodegenerative diseases. Future RCTs are needed to refine treatment choices combining HMB and exercises for older people in particular populations, ages, and health status. Specifically, interventions in older adults aged 80 years or older, with cognitive impairment, frailty, or limited mobility are required.
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http://dx.doi.org/10.3390/nu11092082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769498PMC
September 2019

A Short-Term Response of Soil Microbial Communities to Cadmium and Organic Substrate Amendment in Long-Term Contaminated Soil by Toxic Elements.

Front Microbiol 2018 20;9:2807. Epub 2018 Nov 20.

Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, Prague, Czechia.

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of determined by phylum specific qPCR increased and also the proportion of and increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.
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http://dx.doi.org/10.3389/fmicb.2018.02807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256134PMC
November 2018

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential.

Microbiome 2018 11 22;6(1):208. Epub 2018 Nov 22.

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.

Background: The impacts of man-made chemicals, in particular of persistent organic pollutants, are multifactorial as they may affect the integrity of ecosystems, alter biodiversity and have undesirable effects on many organisms. We have previously demonstrated that the belowground mycobiota of forest soils acts as a buffer against the biocide pollutant pentachlorophenol. However, the trade-offs made by mycobiota to mitigate this pollutant remain cryptic.

Results: Herein, we demonstrate using a culture-dependent approach that exposure to pentachlorophenol led to alterations in the composition and functioning of the metacommunity, many of which were not fully alleviated when most of the biocide was degraded. Proteomic and physiological analyses showed that the carbon and nitrogen metabolisms were particularly affected. This dysregulation is possibly linked to the higher pathogenic potential of the metacommunity following exposure to the biocide, supported by the secretion of proteins related to pathogenicity and reduced susceptibility to a fungicide. Our findings provide additional evidence for the silent risks of environmental pollution, particularly as it may favour the development of pathogenic trade-offs in fungi, which may impose serious threats to animals and plant hosts.
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http://dx.doi.org/10.1186/s40168-018-0589-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251201PMC
November 2018

The Efficacy and Safety of Lower-Limb Plyometric Training in Older Adults: A Systematic Review.

Sports Med 2019 Jan;49(1):113-131

The Strength and Conditioning Laboratory, Department of Physiology and Biochemistry, Faculty of Physical Education and Sport, Charles University, Jose Martiho 269/31, 162 52, Prague 6, Czech Republic.

Background: The aging process is associated with a progressive decline of neuromuscular function, increased risk of falls and fractures, impaired functional performance, and loss of independence. Plyometric training may mitigate or even reverse such age-related deterioration; however, little research on the effects of plyometric exercises has been performed in older adults.

Objective: The objective of this systematic review was to evaluate the safety and efficacy of plyometric training in older adults.

Methods: Papers reporting on randomized trials of plyometric training in older adults (≥ 60 years) and published up to December 2017 were sought in the PubMed, SPORTDiscus, Scopus, and EMBASE databases, and their methodological quality was assessed using the Physiotherapy Evidence Database (PEDro) scale. A narrative synthesis of the findings is presented in this systematic review.

Results: Of the 2236 identified papers, 18 were included in the review, reporting on 12 different studies with a mean PEDro score of 6.0 (range 4-7). Altogether, 289 subjects (176 females and 113 males) were included in 15 intervention groups with plyometric components (n = 8-36 per group); their mean age ranged from 58.4 to 79.4 years. The plyometric training lasted from 4 weeks to 12 months. Muscular strength, bone health, body composition, postural stability, and jump and physical performance were the most often reported outcomes. No study reported increased occurrence of injuries or other adverse events related to plyometric exercises.

Conclusion: Plyometric training is a feasible and safe training option with potential for improving various performance, functional, and health-related outcomes in older persons.
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http://dx.doi.org/10.1007/s40279-018-1018-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349785PMC
January 2019

Field-Based and Lab-Based Assisted Jumping: Unveiling the Testing and Training Implications.

Front Physiol 2018 12;9:1284. Epub 2018 Sep 12.

Department of Physiology and Biochemistry, Faculty of Physical Education and Sport, Charles University, Prague, Czechia.

Assisted jumping can supplement resistance training and traditional plyometric training to increase vertical jump performance. However, as coaches may choose to make field-based decisions based on lab-based research, this study determined whether a field-based assisted jumping set-up results in different ground contact times (CT), take off forces (TOF), flight times (FT), and impact forces (IF) compared to a lab-based set-up. Eighteen active males (24.8 ± 3.0 yr; 178.8 ± 7.8 cm; 77.8 ± 7.8 kg) performed two sessions of assisted jumping: one with each hand holding a commercially available resistance band (1m) that was attached to a pull-up bar (), and the other with assistance from a custom-built system of ropes, pulleys, and long (3 m) elastic bands (). With each set-up, subjects performed five sets of five countermovement jumps on a force plate. Each set was performed with either bodyweight (BW), 90, 80, 70, or 60% of BW, which was achieved by either grabbing higher or lower on the bands during , or by being pulled upward via a full-body harness during . The order of each visit was counter-balanced, and the order of jumps within each visit was quasi-randomized. Data from the 90, 80, 70, and 60% trials for each set-up were then expressed relative to the data of BW jumps, and these relative values were then used for analysis. CT was less than CT at 80, 70, and 60%. FT was greater than FT at 90 and 80%, but FT became greater at 60%. TOF and IF remained unchanged during , but TOF was consistently less than TOF during BW, with IF generally being greater than IF. If the purpose of assisted jumping is to spend less time on the ground without decreasing force, systems with finite adjustments and longer bands like should be used. However, shorter bands similar to may also be used; but due to the larger variability of assistance throughout the range of motion, such systems may alter the neuromuscular characteristics of the jump in other ways that should be investigated in future research.
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http://dx.doi.org/10.3389/fphys.2018.01284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144929PMC
September 2018

Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.

Microb Ecol 2019 Apr 12;77(3):713-725. Epub 2018 Sep 12.

Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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http://dx.doi.org/10.1007/s00248-018-1251-8DOI Listing
April 2019

The concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.

Folia Microbiol (Praha) 2019 Jan 21;64(1):19-23. Epub 2018 Jun 21.

Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, v.v.i., Praha, Czech Republic.

The concept of operational taxonomic units (OTUs), which constructs "mathematically" defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.
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http://dx.doi.org/10.1007/s12223-018-0627-yDOI Listing
January 2019

Discovery of Phloeophagus Beetles as a Source of Strains That Produce Potentially New Bioactive Substances and Description of sp. nov.

Front Microbiol 2018 8;9:913. Epub 2018 May 8.

Microbiology and Genetics Department, University of Salamanca, Salamanca, Spain.

Antimicrobial resistance is a worldwide problem that threatens the effectiveness of treatments for microbial infection. Consequently, it is essential to study unexplored niches that can serve for the isolation of new microbial strains able to produce antimicrobial compounds to develop new drugs. Bark beetles live in phloem of host trees and establish symbioses with microorganisms that provide them with nutrients. In addition, some of their associated bacteria play a role in the beetle protection by producing substances that inhibit antagonists. In this study the capacity of several bacterial strains, isolated from the bark beetles , and , to produce antimicrobial compounds was analyzed. Several isolates exhibited the capacity to inhibit Gram-positive and Gram-negative bacteria, as well as fungi. The genome sequence analysis of three isolates predicted the presence of several gene clusters implicated in the production of already described antimicrobials and moreover, the low similarity of some of these clusters with those previously described, suggests that they encode new undescribed substances, which may be useful for developing new antimicrobial agents. Moreover, these bacteria appear to have genetic machinery for producing antitumoral and antiviral substances. Finally, the strain IA19 showed to represent a new species of the genus . The 16S rRNA gene sequence analysis showed that its most closely related species include and 98.6, 98.5 98.4, and 98.4% identity, respectively. MLSA of the housekeeping genes B, B, and D confirmed that strain IA19 clearly separates from its closest related species. Average nucleotide identity between strains IA19 and ATCC 700689, DSM 11363, KL28 and DSM 17257 were 85.3, 80.2, 79.0, and 72.1%, respectively. Growth occurs at 4-37°C and pH 6.5-8. Optimal growth occurs at 28°C, pH 7-8 and up to 2.5% NaCl. Respiratory ubiquinones are Q9 (97%) and Q8 (3%). C16:0 and in summed feature 3 are the main fatty acids. Based on genotypic, phenotypic and chemotaxonomic characteristics, the description of sp. nov. has been proposed. The type strain is IA19 (=CECT 9403 = LMG 30182).
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http://dx.doi.org/10.3389/fmicb.2018.00913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5953339PMC
May 2018

A pedometer-based walking intervention with and without email counseling in general practice: a pilot randomized controlled trial.

BMC Public Health 2018 05 16;18(1):635. Epub 2018 May 16.

Faculty of Physical Education and Sport, Charles University, Jose Martiho 31, 162 52, Prague 6, Czech Republic.

Background: General practitioners play a fundamental role in combatting the current epidemic of physical inactivity, and pedometer-based walking interventions are able to increase physical activity levels of their patients. Supplementing these interventions with email counseling driven by feedback from the pedometer has the potential to further improve their effectiveness but it has to be yet confirmed in clinical trials. Therefore, the aim of our pilot randomized controlled trial is to evaluate the feasibility and potential efficacy of future trials designed to assess the additional benefit of email counseling added to a pedometer-based intervention in a primary care setting.

Methods: Physically inactive patients were opportunistically recruited from four general practices and randomized to a 12-week pedometer-based intervention with or without email counseling. To explore the feasibility of future trials, we assessed the speed and efficiency of recruitment, adherence to wearing the pedometer, and engagement with email counseling. To evaluate the potential efficacy, daily step-count was the primary outcome and blood pressure, waist and hip circumference, and body mass were the secondary outcomes. Additionally, we conducted a qualitative analysis of structured interviews with the participating general practitioners.

Results: The opportunistic recruitment has been shown to be feasible and acceptable, but relatively slow and inefficient; moreover, general practitioners selectively recruited overweight and obese patients. Patients manifested high adherence, wearing the pedometer on 83% (± 20) of days. All patients from the counseling group actively participated in email communication and responded to 46% (± 22) of the emails they received. Both groups significantly increased their daily step-count (pedometer-plus-email, + 2119, p = 0.002; pedometer-alone, + 1336, p = 0.03), but the difference between groups was not significant (p = 0.18). When analyzing both groups combined, there was a significant decrease in body mass (- 0.68 kg, p = 0.04), waist circumference (- 1.73 cm, p = 0.03), and systolic blood pressure (- 3.48 mmHg, p = 0.045).

Conclusions: This study demonstrates that adding email counseling to a pedometer-based intervention in a primary care setting is feasible and might have the potential to increase the efficacy of such an intervention in increasing physical activity levels.

Trial Registration: The trial was retrospectively registered at ClinicalTrials.gov (ID: NCT03135561 , date: April 26, 2017).
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http://dx.doi.org/10.1186/s12889-018-5520-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956962PMC
May 2018

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses.

Bioinformatics 2018 07;34(13):2292-2294

Institute of Microbiology of the CAS, 14220 Prague 4, Czech Republic.

Motivation: Modern molecular methods have increased our ability to describe microbial communities. Along with the advances brought by new sequencing technologies, we now require intensive computational resources to make sense of the large numbers of sequences continuously produced. The software developed by the scientific community to address this demand, although very useful, require experience of the command-line environment, extensive training and have steep learning curves, limiting their use. We created SEED 2, a graphical user interface for handling high-throughput amplicon-sequencing data under Windows operating systems.

Results: SEED 2 is the only sequence visualizer that empowers users with tools to handle amplicon-sequencing data of microbial community markers. It is suitable for any marker genes sequences obtained through Illumina, IonTorrent or Sanger sequencing. SEED 2 allows the user to process raw sequencing data, identify specific taxa, produce of OTU-tables, create sequence alignments and construct phylogenetic trees. Standard dual core laptops with 8 GB of RAM can handle ca. 8 million of Illumina PE 300 bp sequences, ca. 4 GB of data.

Availability And Implementation: SEED 2 was implemented in Object Pascal and uses internal functions and external software for amplicon data processing. SEED 2 is a freeware software, available at http://www.biomed.cas.cz/mbu/lbwrf/seed/ as a self-contained file, including all the dependencies, and does not require installation. Supplementary data contain a comprehensive list of supported functions.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022770PMC
July 2018

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil.

Microbiome 2017 09 18;5(1):122. Epub 2017 Sep 18.

Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic.

Background: Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process.

Results: Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously.

Conclusions: Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.
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http://dx.doi.org/10.1186/s40168-017-0340-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604414PMC
September 2017