Nejvíce citovaný článek - PubMed ID 20534432
BACKGROUND: Understanding the temporal variability of the microbiome is critical for translating associations of the microbiome with health and disease into clinical practice. The aim of this study is to assess the extent of temporal variability of the human urinary microbiota. A pair of urine samples were collected from study participants at 3-40-month interval. DNA was extracted and the bacterial V4 hypervariable region of the 16S rRNA gene was sequenced on the Illumina MiSeq platform. The alpha diversity of paired samples was analyzed using Chao1 and Shannon indices and PERMANOVA was used to test the factors influencing beta diversity. RESULTS: A total of 63 participants (43 men and 20 women with a mean age of 63.0 and 57.1 years, respectively) were included in the final analysis. An average of 152 ± 128 bacterial operational taxonomic units (OTUs) were identified in each urine sample from the entire cohort. There was an average of 41 ± 32 overlapping OTUs in each sample pair, accounting for 66.3 ± 29.4% of the relative abundance. There was a clear correlation between the number of overlapping OTUs and the relative abundance covered. The difference in Chao1 index between paired samples was statistically significant; the difference in Shannon index was not. Beta diversity did not differ significantly within the paired samples. Neither age nor sex of the participants influenced the variation in community composition. With a longer interval between the collections, the relative abundance covered by the overlapping OTUs changed significantly but not the number of OTUs. CONCLUSION: Our findings demonstrated that, while the relative abundance of dominant bacteria varied, repeated collections generally shared more than 60% of the bacterial community. Furthermore, we observed little variation in the alpha and beta diversity of the microbial community in human urine. These results help to understand the dynamics of human urinary microbiota and enable interpretation of future studies.
- Klíčová slova
- 16S rRNA gene, Bacterial community, Next-generation sequencing, Stability, Urinary microbiota, Variability,
- MeSH
- Bacteria * klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- časové faktory MeSH
- DNA bakterií genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- mikrobiota * genetika MeSH
- moč * mikrobiologie MeSH
- prospektivní studie MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- Názvy látek
- DNA bakterií MeSH
- RNA ribozomální 16S MeSH
In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.
- Klíčová slova
- 16S rRNA gene, Asgard archaea, aquatic sediments, archaeal diversity, microbial ecology,
- Publikační typ
- časopisecké články MeSH
Little is known about how zoonotic virus infections manifest in wildlife reservoirs. However, a common health consequence of enteric virus infections is gastrointestinal diseases following a shift in gut microbial composition. The sub-Saharan hipposiderid bat complex has recently emerged to host at least three coronaviruses (CoVs), with Hipposideros caffer D appearing particularly susceptible to Hibecovirus CoV-2B infection. In this study, we complement body condition and infection status data with information about the gut microbial community to understand the health impact of CoV infections in a wild bat population. Of the three CoVs, only infections with the distantly SARS-related Hibecovirus CoV-2B were associated with lower body condition and altered the gut microbial diversity and composition. The gut microbial community of infected bats became progressively less diverse and more dissimilar with infection intensity, arguing for dysbiosis as per the Anna Karenina principle. Putatively beneficial bacteria, such as Alistipes and Christensenella, decreased with infection intensity, while potentially pathogenic bacteria, namely Mycoplasma and Staphylococcus, increased. Infections with enterically replicating viruses may therefore cause changes in body condition and gut dysbiosis with potential negative health consequences even in virus reservoirs. We argue that high-resolution data on multiple health markers, ideally including microbiome information, will provide a more nuanced picture of bat disease ecology.
- Klíčová slova
- Anna Karenina principle, Chiroptera, Ghana, coronavirus, microbiome,
- Publikační typ
- časopisecké články MeSH
PREMISE: Despite the high functional importance of endophytes, we still have limited understanding of the biotic and abiotic factors that influence colonization of plant hosts along major ecological gradients and lack quantitative estimates of their colonization extent. In this study, we hypothesized that the developmental stage of the ecosystem will affect the levels of bacterial and fungal endophytic assemblages in the foliar endosphere. METHODS: We quantified levels of bacterial and fungal endophytes in leaves of four plant hosts at four stages of vegetation succession using an optimized qPCR protocol with bacteria-specific 16S and fungi-targeting primers. RESULTS: (1) The ecosystem developmental stage did not have a significant effect on the colonization levels of bacterial or fungal endophytes. (2) Colonization levels by bacterial and fungal endophytes were governed by different mechanisms. (3) Endophytic colonization levels and their relationship to foliar tissue stoichiometry were highly host specific. CONCLUSIONS: Quantifying colonization levels is important in the study of endophytic ecology, and the fast, relatively low-cost qPCR-based method can supply useful ecological information, which can significantly enhance the interpretation potential of descriptive data generated, for example, by next-generation sequencing.
- Klíčová slova
- cell counts, ecological succession, foliar endophyte, fungi‐bacteria ratios, qPCR, soil chronosequence,
- MeSH
- Bacteria * genetika růst a vývoj izolace a purifikace MeSH
- ekosystém MeSH
- endofyty * fyziologie genetika MeSH
- hostitelská specificita * MeSH
- houby * genetika izolace a purifikace fyziologie MeSH
- kvantitativní polymerázová řetězová reakce metody MeSH
- listy rostlin * mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
Understanding the intricate dynamics of sediment-mediated microbial interactions and their impact on plant tissue preservation is crucial for unraveling the complexities of leaf decay and preservation processes. To elucidate the earliest stages of leaf preservation, a series of decay experiments was carried out for three months on Nymphaea water lily leaves in aquariums with pond water and one of three distinctly different, sterilized, fine-grained substrates-commercially purchased kaolinite clay or fine sand, or natural pond mud. One aquarium contained only pond water as a control. We use 16S and ITS rRNA gene amplicon sequencing to identify and characterize the complex composition of the bacterial and fungal communities on leaves. Our results reveal that the pond mud substrate produces a unique community composition in the biofilms compared to other substrates. The mud substrate significantly influences microbial communities, as shown by the correlation between high concentrations of minerals in the water and bacterial abundance. Furthermore, more biofilm formers are observed on the leaves exposed to mud after two months, contrasting with declines on other substrates. The mud substrate also enhanced leaf tissue preservation compared to the other sediment types, providing insight into the role of sediment and biofilms in fossilization processes. Notably, leaves on kaolinite clay have the fewest biofilm formers by the end of the experiment. We also identify key biofilm-forming microbes associated with each substrate. The organic-rich mud substrate emerges as a hotspot for biofilm formers, showing that it promotes biofilm formation on leaves and may increase the preservation potential of leaves better than other substrates. The mud's chemical composition, rich in minerals such as silica, iron, aluminum, and phosphate, may slow or suspend decay and facilitate biomineralization, thus paving the way toward leaf preservation. Our study bridges the information gap between biofilms observed on modern leaves and the mineral encrustation on fossil leaves by analyzing the microbial response in biofilms to substrate types in which fossil leaves are commonly found.
Microbial colonization on the titanium condenser material (TCM) used in the cooling system leads to biofouling and corrosion and influences the water supply. The primary investigation of the titanium condenser was infrequently studied on characterizing biofilm-forming bacterial communities. Different treatment methods like electropotential charge, ultrasonication, and copper coating of titanium condenser material may influence the microbial population over the surface of the titanium condensers. The present study aimed to catalog the primary colonizers and the effect of different treatment methods on the microbial community. CFU (1.7 × 109 CFU/mL) and ATP count (< 5000 × 10-7 relative luminescence units) showed a minimal microbial population in copper-coated surface biofilm as compared with the other treatments. Live and dead cell result also showed consistency with colony count. The biofilm sample on the copper-coated surface showed an increased dead cell count and decreased live cells. In the metagenomic approach, the microbiome coverage was 10.06 Mb in samples derived from copper-coated TCM than in other treated samples (electropotential charge-17.94 Mb; ultrasonication-20.01 Mb), including control (10.18 Mb). Firmicutes preponderate the communities in the biofilm samples, and Proteobacteria stand next in the population in all the treated condenser materials. At the genus level, Lactobacillaceae and Azospirillaceae dominated the biofilm community. The metagenome data suggested that the attached community is different from those biofilm samples based on the environment that influences the bacterial community. The outcome of the present study depicts that copper coating was effective against biofouling and corrosion resistance of titanium condenser material for designing long-term durability.
- Klíčová slova
- Bacterial community, MEGAN, Metagenome, QIIME 2, Titanium condenser,
- MeSH
- Bacteria * genetika klasifikace izolace a purifikace MeSH
- biofilmy * růst a vývoj MeSH
- měď farmakologie MeSH
- metagenomika * MeSH
- mikrobiologie vody MeSH
- mikrobiota MeSH
- titan * chemie MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- měď MeSH
- titan * MeSH
In the first days of life, the newborns' intestinal microbiota develops simultaneously with the intestinal gut barrier and follows intestinal immunity. The mode of delivery shows significant impact on microbial development and, thus, the initiation of the tryptophan catabolism pathway. Further antibiotics (ATB) treatment of mothers before or during delivery affects the microbial and tryptophan metabolite composition of stool of the caesarean- and vaginal-delivered newborns. The determination of microbiome and levels of tryptophan microbial metabolites in meconium and stool can characterize intestinal colonization of a newborn. From 134 samples from the Central European Longitudinal Studies of Parents and Children: The Next Generation (CELSPAC: TNG) cohort study, 16S rRNA gene sequencing was performed, and microbial tryptophan metabolites were quantified using ultra-high-performance liquid chromatography with triple-quadrupole mass spectrometry. Microbial diversity and concentrations of tryptophan metabolites were significantly higher in stool compared to meconium. Treatment of mothers with ATB before or during delivery affects metabolite composition and microbial diversity in stool of vaginal- and caesarean-delivered newborns. Correlation of microbial and metabolite composition shows significant positive correlations of indol-3-lactic acid, N-acetyl-tryptophan and indol-3-acetic acid with Bifidobacterium, Bacteroides and Peptoclostridium. The positive effect of vaginal delivery on newborns' microbiome development is degraded when mother is treated with ATB before or during delivery. KEY POINTS: • Antibiotic treatment diminishes the positive effects of vaginal delivery. • Antibiotic treatment affects metabolite and microbial composition in newborns. • Bifidobacterium and Peptoclostridium could be the producer of indole-lactic acid.
- Klíčová slova
- Caesarean delivery, Kynurenine, Microbiome, Stool, Tryptophan catabolites, Vaginal delivery,
- MeSH
- antibakteriální látky * MeSH
- Bifidobacterium metabolismus růst a vývoj MeSH
- feces * mikrobiologie chemie MeSH
- indoly metabolismus MeSH
- kyseliny indoloctové metabolismus MeSH
- lidé MeSH
- longitudinální studie MeSH
- mekonium * mikrobiologie chemie MeSH
- novorozenec MeSH
- RNA ribozomální 16S * genetika MeSH
- střevní mikroflóra * účinky léků MeSH
- tryptofan * metabolismus MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- Check Tag
- lidé MeSH
- novorozenec MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antibakteriální látky * MeSH
- indole-3-lactic acid MeSH Prohlížeč
- indoleacetic acid MeSH Prohlížeč
- indoly MeSH
- kyseliny indoloctové MeSH
- RNA ribozomální 16S * MeSH
- tryptofan * MeSH
More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.
- MeSH
- Archaea klasifikace genetika MeSH
- Bacteria klasifikace genetika MeSH
- bezobratlí klasifikace MeSH
- biodiverzita * MeSH
- geologické sedimenty mikrobiologie MeSH
- houby klasifikace genetika MeSH
- řeky * mikrobiologie MeSH
- rostliny klasifikace MeSH
- taxonomické DNA čárové kódování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Intrapartum antibiotic prophylaxis (IAP) is commonly used during C-section delivery and in Group B Streptococcus-positive women before vaginal delivery. Here, we primarily aimed to investigate the effect of IAP on the neonatal oral and fecal bacteriomes in the first week of life. In this preliminary study, maternal and neonatal oral swabs and neonatal fecal (meconium and transitional stool) swabs were selected from a pool of samples from healthy mother-neonate pairs participating in the pilot phase of CELSPAC: TNG during their hospital stay. The DNA was extracted and bacteriome profiles were determined by 16S rRNA amplicon sequencing (Illumina). In the final dataset, 33 mother-neonate pairs were exposed to antibiotics during C-section or vaginal delivery (cases; +IAP) and the vaginal delivery without IAP (controls, -IAP) took place in 33 mother-neonate pairs. Differences in alpha diversity (Shannon index, p=0.01) and bacterial composition (PERMANOVA, p<0.05) between the +IAP and -IAP groups were detected only in neonatal oral samples collected ≤48 h after birth. No significant differences between meconium bacteriomes of the +IAP and -IAP groups were observed (p>0.05). However, the IAP was associated with decreased alpha diversity (number of amplicon sequence variants, p<0.001), decreased relative abundances of the genera Bacteroides and Bifidobacterium, and increased relative abundances of genera Enterococcus and Rothia (q<0.01 for all of them) in transitional stool samples. The findings of this study suggest that exposure to IAP may significantly influence the early development of the neonatal oral and gut microbiomes. IAP affected the neonatal oral bacteriome in the first two days after birth as well as the neonatal fecal bacteriome in transitional stool samples. In addition, it highlights the necessity for further investigation into the potential long-term health impacts on children.
- Klíčová slova
- 16S rRNA, Antibiotics, Diversity, Infant, Microbiome, Mother, Next-generation sequencing,
- MeSH
- antibakteriální látky * aplikace a dávkování MeSH
- antibiotická profylaxe * metody MeSH
- Bacteria genetika klasifikace izolace a purifikace účinky léků MeSH
- císařský řez MeSH
- dospělí MeSH
- feces * mikrobiologie MeSH
- lidé MeSH
- mekonium mikrobiologie MeSH
- novorozenec MeSH
- RNA ribozomální 16S genetika MeSH
- střevní mikroflóra účinky léků MeSH
- těhotenství MeSH
- ústa * mikrobiologie MeSH
- vedení porodu MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antibakteriální látky * MeSH
- RNA ribozomální 16S MeSH
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
- Klíčová slova
- abiotic factors, freshwater environments, prokaryotes, protists, stratification, temporal dynamics,
- MeSH
- Bacteria * genetika klasifikace MeSH
- biodiverzita MeSH
- časoprostorová analýza MeSH
- ekosystém MeSH
- Eukaryota * genetika klasifikace MeSH
- jezera * mikrobiologie MeSH
- mikrobiota * MeSH
- roční období MeSH
- strojové učení * MeSH
- taxonomické DNA čárové kódování * MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
