Heterogeneity Spacers in 16S rDNA Primers Improve Analysis of Mouse Gut Microbiomes via Greater Nucleotide Diversity

Jensen, Elizabeth; Berryman, Darlene E.; Murphy, Erin R.; Carroll, Rachel; Busken, Joshua; List, Edward O.; Broach, William H.

doi:10.2144/btn-2019-0025

Cited by 15 publications

(14 citation statements)

References 24 publications

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“…The fact that we did not explicitly detect B. subtilis and B. licheniforms, the major components in the probiotic preparation, may be due to the relatively short V3-V4 amplicon sequences, not allowing discrimination between closely related species [33]. Our result that the probiotic bacteria consumed by the ducks with their feed did not reside in the gut complies with the fact that Bacillus representatives are not common for the gut microbiota of poultry [31,34].…”

Section: Discussionsupporting

confidence: 69%

Bacillus-Based Probiotic Treatment Modified Bacteriobiome Diversity in Duck Feces

et al. 2021

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The intestinal health of poultry is of great importance for birds’ growth and development; probiotics-driven shifts in gut microbiome can exert considerable indirect effect on birds’ welfare and production performance. The information about gut microbiota of ducks is scarce; by using high throughput metagenomic sequencing with Illumina Miseq we examined fecal bacterial diversity of Peking ducks grown on conventional and Bacillus-probiotic-enriched feed. The probiotic supplementation drastically decreased the presence of the opportunistic pathogen Escherichia/Shigella, which was the major and sole common dominant in all samples. Seventy other bacterial species in the ducks’ fecal assemblages were found to have probiotic-related differences, which were interpreted as beneficial for ducks’ health as was confirmed by the increased production performance of the probiotic-fed ducks. Bacterial α-biodiversity indices increased in the probiotic-fed group. The presented inventory of the duck fecal bacteriobiome can be very useful for the global meta-analysis of similar data in order to gain a better insight into bacterial functioning and interactions with other gut microbiota to improve poultry health, welfare and production performance.

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Section: Discussionsupporting

confidence: 69%

Bacillus-Based Probiotic Treatment Modified Bacteriobiome Diversity in Duck Feces

et al. 2021

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“…Bioinformatic analysis of the obtained sequencing for taxonomic identification was performed according to Jensen et al [ 32 ]. Bioinformatic analysis was carried out using CLC Genomic Workbench v. 12 (Qiagen, Hilden, Germany) + Microbial Genomics Module Plugin v. 4.1 (Qiagen).…”

Section: Methodsmentioning

confidence: 99%

Assessment of Dust, Chemical, Microbiological Pollutions and Microclimatic Parameters of Indoor Air in Sports Facilities

Szulc

Cichowicz

Gutarowski

et al. 2023

IJERPH

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The aim of this study was to analyse the quality of indoor air in sport facilities in one of the sport centres in Poland with respect to microclimatic parameters (temperature, humidity, and air flow velocity), particulate matter concentrations (PM10, PM4, PM2.5, and PM1), gas concentrations (oxygen, ozone, hydrogen sulphide, sulphur dioxide, volatile organic compounds, and benzopyrene), and microbial contamination (the total number of bacteria, specifically staphylococci, including Staphylococcus aureus, haemolytic bacteria, Enterobacteriaceae, Pseudomonas fluorescens, actinomycetes, and the total number of fungi and xerophilic fungi). Measurements were made three times in May 2022 at 28 sampling points in 5 different sporting areas (the climbing wall, swimming pool, swimming pool changing room, and basketball and badminton courts) depending on the time of day (morning or afternoon) and on the outside building. The obtained results were compared with the standards for air quality in sports facilities. The air temperature (21–31 °C) was at the upper limit of thermal comfort, while the air humidity (RH < 40%) in the sports halls in most of the locations was below demanded values. The values for dust pollution in all rooms, except the swimming pool, exceeded the permissible limits, especially in the afternoons. Climatic conditions correlated with a high concentration of dust in the indoor air. Particulate matter concentrations of all fractions exceeded the WHO guidelines in all researched premises; the largest exceedances of standards occurred for PM2.5 (five-fold) and for PM10 (two-fold). There were no exceedances of gaseous pollutant concentrations in the air, except for benzopyrene, which resulted from the influence of the outside air. The total number of bacteria (5.1 × 101–2.0 × 104 CFU m−3) and fungi (3.0 × 101–3.75 × 102 CFU m−3) was exceeded in the changing room and the climbing wall hall. An increased number of staphylococci in the afternoon was associated with a large number of people training. The increased concentration of xerophilic fungi in the air correlated with the high dust content and low air humidity. Along with the increase in the number of users in the afternoon and their activities, the concentration of dust (several times) and microorganisms (1–2 log) in the air increased by several times and 1–2 log, respectively. The present study indicates which air quality parameters should be monitored and provides guidelines on how to increase the comfort of those who practice sports and work in sports facilities.

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“…However, designing index adaptors or primers comprising different variable-length sequences can be a complicated and challenging approach with additional technical limitations [154]. However, this approach has been tested for multiple targets and allowed for an increased reads recovery and increased base quality at the 3′ end [155][156][157][158]. Another possibility to increase the base diversity is to sequence multiple targets in the same sequencing run (i.e., 16S, 18S and ITS gene libraries of the same samples), which is pertinent in research projects interested in multiple target taxa but should be restricted to marker gene of comparable length.…”

Section: Further Recommendations For Library Preparationmentioning

confidence: 99%

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

et al. 2021

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Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

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Heterogeneity Spacers in 16S rDNA Primers Improve Analysis of Mouse Gut Microbiomes via Greater Nucleotide Diversity

Cited by 15 publications

References 24 publications

Bacillus-Based Probiotic Treatment Modified Bacteriobiome Diversity in Duck Feces

Bacillus-Based Probiotic Treatment Modified Bacteriobiome Diversity in Duck Feces

Assessment of Dust, Chemical, Microbiological Pollutions and Microclimatic Parameters of Indoor Air in Sports Facilities

DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

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