• Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology. (frontiersin.org)
  • These skills are applied to microbial ecology, probiotics, metagenomics and microbial functional genomics. (massey.ac.nz)
  • General and enviromental microbiology researcher and PI with independent research programme in microbial ecology, metagenomics, host-microbial interactions and bacteriophage-related technologies. (massey.ac.nz)
  • Although the advent of sequencing technologies has fostered our understanding of the processes and factors shaping bacterial assemblages, there are still limitations among microbial ecology studies: e.g., most research is ecosystem-specific, neglecting the dispersal of microbes across different habitats or local communities. (aiol.info)
  • It can be used to explore the diversity, function, and ecology of microbial communities. (bioinformatics.ca)
  • Specific diseases of interest include common conditions of pregnancy, gut microbial ecology and Necrotizing Enterocolitis (NEC). (stanford.edu)
  • Identification of sulfate-reducing and methanogenic microbial taxa in anaerobic bioreactors from industrial wastewater treatment plants using next-generation sequencing and gene clone library analyses. (cri.or.th)
  • We analyzed the vertical profiles of microbial biomass indicators (PLFAs, DNA and RNA) and the bacterial and archaeal community composition (sequencing of 16S rRNA gene amplicons and qPCR of mcrA) in sediment cores collected from a typical small boreal lake. (scilifelab.se)
  • Although anaerobic microorganisms containing the hgcA gene potentially mediate the formation of methylmercury in natural environments, the diversity of these mercury-methylating microbial communities remains largely unexplored. (scilifelab.se)
  • Microbial communities within deep subsurface environments were analyzed by 16S rRNA gene cloning. (princeton.edu)
  • Molecular- taxa identified by 16S rRNA gene sequencing, the associa- based approaches to pathogen detection enhance the ability tion between pathogen and disease was decreased, which to quantify the abundance of pathogens shed in the stool. (cdc.gov)
  • We investigated the relationship of the microbiome with the neuroanatomy and cognitive function of 281 healthy children in a cross-sectional analysis and demonstrated that differences in gut microbial taxa and gene functions are associated with the size of brain regions and with overall cognitive function. (biorxiv.org)
  • Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. (biomedcentral.com)
  • 16S rRNA gene sequencing was used to measure sample-level microbial communities. (cdc.gov)
  • Similarly, we can contextualize taxa and gene abundance data of microbial communities with the structural elements of their genome. (fems-microbiology.org)
  • 2019. SSU-rRNA gene sequencing survey of benthic microbial eukaryotes from Guaymas Basin hydrothermal vent. (usc.edu)
  • Clear and concise, this easy-to-use book offers an introductory course on the language of gene cloning, covering microbial, plant, and mammalian systems. (lu.se)
  • While microbial responses to experimental droughts were weak, scant rainfall periods resulted in decreased microbial biomass and activity, and relative abundances of bacterial groups such as Proteobacteria, Verrucomicrobia, and Acidobacteria decreased concomitantly with increases in Actinobacteria, Chloroflexi, and Firmicutes abundance. (nature.com)
  • More importantly, the abundance of microbial taxa was markedly differentiated at the low (1.5 g/kg) and high (3.0 g/kg) dose of spirulina , among which the relative abundance of Clostridium XIVa, Desulfovibrio, Eubacterium, Barnesiella, Bacteroides , and Flavonifractor were modulated at various degrees. (frontiersin.org)
  • Microbial diversity and relative abundance of Streptococcus , Prevotella and Veillonella were inversely associated with airway inflammation. (ersjournals.com)
  • For instance, MMKD increased the relative abundance of bacterial taxa Enterobacteriaceae, Akkermansia , etc., and Agaricus and Mrakia fungal species in MCI patients. (news-medical.net)
  • Differential abundance of taxa were identified between O157(+) and O157(-) samples and between shedding days of individuals, using matched Wilcoxon rank-sum tests, zero-inflated Gaussian (ZIG) regression and negative binomial regression. (cdc.gov)
  • In recent years metagenomics led to notable breakthroughs in describing this microbial diversity, yet 50-90% of species are typically present at too low abundance to be genome or strain resolved. (europa.eu)
  • Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds. (scilifelab.se)
  • The goal of this study was to determine whether the microbiome from Parkinson's disease (PD) has alterations in a) Polyamine metabolism and b) Expressed taxa of intestinal bacterial. (mdsabstracts.org)
  • and (2) that the development of host-free microbiome model systems could be useful for rapidly screening pesticides against functionally distinct microbial catalogues of interest. (researchgate.net)
  • The gut microbial community is seeded at birth, and develops over the course of the first year from a low-diversity community dominated by Firmicutes and Proteobacteria, to a more diverse, adult-like microbiome upon the introduction of solid food. (biorxiv.org)
  • Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. (biomedcentral.com)
  • These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. (biomedcentral.com)
  • Much of this information has been derived from isolated bacteria and less is known about how these traits are distributed among microbial communities. (fems-microbiology.org)
  • In the present study, we characterized the diversity of mercury-methylating microbial communities of boreal lake sediments using high-throughput sequencing of 16S rRNA and hgcA genes. (scilifelab.se)
  • Borehole fluids derived from deep fractures were populated by microbial communities with low diversity with an average of 11 and 5 bacterial and archaeal OTUs respectively. (princeton.edu)
  • Based on the analysis of 16s rDNA sequencing, compared to the saline-treated group, oral administration of spirulina once daily for 24 consecutive days altered the diversity, structure, and composition of colonic microbial community at the genus level. (frontiersin.org)
  • Conclusions: Microbial diversity and some taxa may be influenced by or affect O157 shedding by dairy cattle. (cdc.gov)
  • Microbial diversity was characterized using alpha diversity patterns. (cdc.gov)
  • Determine which microbes are the source of microbial lactase in genetically intolerant people. (cdrf.org)
  • While microbial biomass decreased with sediment depth, viable microbes (RNA and PLFA) were present all through the profiles. (scilifelab.se)
  • Corrigendum to "Exploring the secretomes of microbes and microbial communities using filamentous phage display" [Front. (massey.ac.nz)
  • During the past years we have explored the biogeography of bacteria considering this potential connectivity among communities, unveiling a major role of microbial dispersal in fresh- and marine waters: We have shown that boreal lakes and rivers are strongly influenced by the transport of taxa from the surrounding terrestrial landscape, and that deep ocean communities seem largely structured by the sinking of surface microbes attached to particles. (aiol.info)
  • The genetic information of a microbial community - known as the metagenome - provides a glimpse into the genetic potential of microbes in their natural environment. (fems-microbiology.org)
  • The study " Variation in genomic traits of microbial communities among ecosystems " published in FEMS Microbes analyzes these traits from available metagenomes from different microbial communities. (fems-microbiology.org)
  • Based on this, the study " Variation in genomic traits of microbial communities among ecosystems" published in FEMS Microbes determines how genomic traits are distributed among bacterial-dominated microbial communities. (fems-microbiology.org)
  • The project will characterise the evolution of long-term human-associated eukaryotes and prokaryotes, using high-precision metagenomics of elusive microbes, studying the microbial genetics of their gastrointestinal persistence, and estimating pro- and eukaryotic strain persistence across human generations. (europa.eu)
  • Like microbial communities at other body sites, the oral microbiota comprises both health- and disease-promoting microbes (commensals and pathogens). (ccf.org)
  • The changes induced to microbial communities by the addition of Fe3+ and Mn4+ were studied using next-generation sequencing targeting the 16S rRNA and methyl-coenzyme M reductase (mcrA) genes and mcrA transcripts. (scilifelab.se)
  • Our findings provide a mechanistic bridge between microbial community structure at different levels of organization, and show that the evolutionary conservation of metabolic traits, both in terms of growth responses and niches constructed, can be leveraged to quantitatively predict the taxonomic and metabolic structure of microbial communities. (biorxiv.org)
  • An international team of researchers has developed a new method to investigate the structure of microbial communities that attach themselves to microplastic trash, a significant concern to marine biologists. (azocleantech.com)
  • Although sediments of small boreal humic lakes are important carbon stores and greenhouse gas sources, the composition and structuring mechanisms of their microbial communities have remained understudied. (scilifelab.se)
  • We observed that the removal of snow increased light penetration through the ice, increasing water temperature and modifying microbial composition in the different depths. (scilifelab.se)
  • Seasonal differences in the community composition of bacteria and phytoplankton were mainly related to changes in observed taxa, while the differences across nutrient treatments within an experiment were due to changes in relative contributions of certain higher- and lower-level phylogenetic groups. (scilifelab.se)
  • Here, we investigated the effects of extreme drought and exotic plants, two of the most significant threats to Mediterranean-type ecosystems, on soil microbial community composition and carbon metabolic genes within a four-year field rainfall manipulation experiment. (nature.com)
  • Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism), but the influence of gut microbial metabolism on typical neurodevelopment has not been explored in detail. (biorxiv.org)
  • As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. (biomedcentral.com)
  • We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. (whiterose.ac.uk)
  • There was moderate concordance between soil microbial communities and plant species composition within microsites. (whiterose.ac.uk)
  • Yet, these studies also find that the taxonomic composition (at the genus or lower level) is highly variable amongst replicate habitats, and this variability was also strong when grouping taxa by their ability to perform specific metabolic pathways (i.e. within functional groups). (biorxiv.org)
  • Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the open ocean. (usc.edu)
  • AIM: To determine the efficacy of a low FODMAP diet in childhood IBS and whether gut microbial composition and/or metabolic capacity are associated with its efficacy. (medscape.com)
  • Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. (medscape.com)
  • Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. (scilifelab.se)
  • Relationships found between microbial taxonomic groups and carbon metabolic genes support the interpretation that exotic plants change microbial carbon cycling by altering the soil microclimate and supplying easily decomposed high-quality litter. (nature.com)
  • EPYC will develop the next-generation of high-resolution metagenomics of an extended taxonomic range, enabling me to research microbial evolution in the human gut. (europa.eu)
  • The results also suggested that, similar to marine systems, the deep bacterial and archaeal communities were predominantly assembled by selective survival of taxa able to persist in the low energy conditions. (scilifelab.se)
  • Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes. (scilifelab.se)
  • Our results significantly increase our knowledge on the microbial communities and their metabolic potential in oxygen-depleted freshwaters and help to understand and predict how climate change-induced alterations could impact the lake carbon dynamics. (scilifelab.se)
  • As carbon of terrestrial origin is increasing in subarctic freshwaters the resource pool supporting their microbial communities and metabolism is changing, with consequences to overall aquatic productivity. (scilifelab.se)
  • These systems typically stratify in summer and their hypolimnetic microbial communities influence burial of biogenic organic matter in sediments. (scilifelab.se)
  • Significant gaps in our understanding of how global change drivers interact to affect the resistance and functioning of microbial communities hinders our ability to model ecosystem responses and feedbacks to co-occurring global stressors. (nature.com)
  • This is partly because bacterial communities harbour thousands of taxa with very different lifestyles, persistence and dispersal capacities. (aiol.info)
  • In addition, by modelling the spatial distribution of individual bacterial taxa, we have identified specific behaviours within aquatic prokaryotes, which can in turn be used to understand underlying processes linked to local selection or passive dispersal, or how environmental fluctuations regulate the relative abundances of generalist and specialist taxa across communities. (aiol.info)
  • Vector fitting of community-weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon-to-nitrogen ratios, and leaf dry matter content. (whiterose.ac.uk)
  • Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long-term climate change effects, especially in nutrient-poor systems with slow-growing vegetation. (whiterose.ac.uk)
  • Microbial communities associated with indoor dust abound in the built environment. (biomedcentral.com)
  • Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. (biomedcentral.com)
  • This makes it possible to capture the interactions between plants and microbial communities. (ncl.ac.uk)
  • To develop a quantitative theory that can predict how microbiomes assemble, and how they respond to perturbations, we must identify which descriptive features of microbial communities are reproducible and predictable, which are unpredictable, and why. (biorxiv.org)
  • By studying the self-assembly of hundreds of communities in replicate, synthetic habitats, we show that the reproducibility of microbial community assembly reflects an emergent metabolic structure, which is quantitatively predictable from first-principles, genome-scale metabolic models. (biorxiv.org)
  • This goal calls for us to identify the quantitative rules governing assembly of microbial communities at different levels of organization. (biorxiv.org)
  • We aimed to measure faecal microbial communities in early lactation dairy cattle, and model outcomes with O157 shedding metrics. (cdc.gov)
  • FEMSmicroBlog: What shapes genomic traits in microbial communities? (fems-microbiology.org)
  • Additionally, host-associated microbial communities were both small and AT-rich, consistent with findings from isolates. (fems-microbiology.org)
  • Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. (oregonstate.edu)
  • Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
  • In relation to the spatial structure of the Plastisphere, scientists found that the microbial communities were mixed heterogeneously, allowing for inferences to be drawn about the interactions on marine microplastics. (azocleantech.com)
  • Evaluation of serum biomarkers in mice at the end of spirulina intervention showed reduced the oxidative stress and the blood lipid levels and increased the level of appetite controlling hormone leptin in a dose-response manner, which exhibited the significant correlation with differentially abundant microbiota taxa in the cecum. (frontiersin.org)
  • Negative binomial models and Wilcoxon tests revealed no differentially abundant taxa between O157(+) vs O157(-) samples, or between shedding days of individuals. (cdc.gov)
  • Streptococcus , Prevotella and Veillonella ) constituted ∼50% of the microbiota, whereas in CF patients aged ≥6 years, traditional CF taxa ( e.g . (ersjournals.com)
  • In the bottom waters, rare and poorly characterized taxa, such as ε-Proteobacteria, but also autotrophs, such as photolithotrophic Chlorobia were abundant. (scilifelab.se)
  • Additionally, 3 coabundance factors were determined for the 25 most abundant taxa. (cdc.gov)
  • Besides their central role as emitters of greenhouse gases, we have only recently begun to understand the microbial systems driving the metabolic processes and elemental cycles in these lakes. (scilifelab.se)
  • IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. (biomedcentral.com)
  • Responders were enriched at baseline in taxa with known greater saccharolytic metabolic capacity (e.g. (medscape.com)
  • Because it can be applied to environmental samples, the approach we present is broadly applicable to measuring population growth, mortality, and associated biogeochemical process rates of microbial taxa for a wide range of ecosystems and can help reveal how individual microbial populations drive biogeochemical fluxes. (osti.gov)
  • Additionally, microbial heterotrophic respiration is one of the largest avenues of C loss from ecosystems [ 21 ]. (nature.com)
  • Similarly, phytoplankton species from the same genera responded differently to nutrient amendments even though biovolumes of the majority of taxa increased when both nitrogen and phosphorus were added simultaneously. (scilifelab.se)
  • Jakoba is a genus in the taxon Excavata, and currently has a single described species, Jakoba libera described by Patterson in 1990, and named in honour of Dutch botanist (Algology, Myology and Lichenology) Jakoba Ruinen. (wikipedia.org)
  • First developed by the Biologist Dr Paul D. N. Hebert, DNA barcoding uses DNA sequences as taxon 'barcodes' to identify species. (ncl.ac.uk)
  • More than 200 microbial species inhabit each human gut and are important for human health, supporting nutrition, pathogen defence and immune homeostasis. (europa.eu)
  • Yu and colleagues (2019) 3 were able to effectively combine multi-omics data to analyze a microbial community's ability to break down bisphenol A (BPA) products. (rsc.org)
  • Through a clever multi-omics design, the authors were able to use three major types of integrated analyses to identify differences in encoded and expressed microbial functions that were involved in the BPA-degrading microbial community. (rsc.org)
  • We identified many microbial taxa whose abundances were influenced by host genetics. (nih.gov)
  • Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. (whiterose.ac.uk)
  • simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community. (biomedcentral.com)
  • Microbial enzymes involved in the metabolism of neuroactive compounds such as glutamate and GABA, were also associated with structure of the brain, including the first brain regions to develop such as the cerebellum, and with overall cognitive function. (biorxiv.org)
  • Soil microbial community responses to drought and exotic plants could potentially impact ecosystem C storage by producing a smaller, more vulnerable C pool of microbial biomass that is prone to increased pulses of heterotrophic respiration. (nature.com)
  • 0.05) of taxa for Akkermansia muciniphila, Porphyromonas bennonis, Ruminococcus bromii, Methanobrevibacter smithii , and Bifidobacterium adolescentis as compared to the Healthy cohort. (mdsabstracts.org)
  • Low taxa richness was likely driven by limited biogeochemical reactions available for growth and not extreme parameters such as pH and temperature. (princeton.edu)
  • Taxa and their spatial distribution were identified and visualized simultaneously in a number of experiments investigating three different biogeographical regions. (azocleantech.com)
  • In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. (scilifelab.se)
  • We combined measurements of bulk microbial and soil properties with high-throughput microbial community analyses to elucidate microbial responses and microbial-mediated alterations to carbon cycling. (nature.com)
  • Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat. (nih.gov)
  • Moreover, the MMKD significantly affected gut microbial populations, including mycobiome and stool metabolites. (news-medical.net)
  • The ecological balance between these taxa - and thus host susceptibility to disease - is strongly shaped by host-derived metabolites. (ccf.org)
  • These topology features of the cooccurrence networks point toward microbial community dynamics being resistant over time and thus could provide indicators for the state of ecosystem stability. (scilifelab.se)
  • Microbial community of biofeed for marbling of beef meat (01/08/2020) Microbiological and genomic characterization of samples of micro-biofeed mixtures used to produce marble beef and isolation of dominant bacteria strains. (massey.ac.nz)
  • Sequencing detected a dominant taxon not traditionally associated with CF ( e.g . (ersjournals.com)
  • Instead, the increased EA availability suppressed CH4 production via the outcompetition of methanogens by anaerobically respiring bacteria and via the increased protection of organic matter from microbial degradation induced by Fe3+ and Mn4+. (scilifelab.se)
  • In contrast to short-term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. (whiterose.ac.uk)
  • Seventy-one strains showed an anti-microbial activity against S. mutans, one strain against S. aureus and none against C. albicans or E. faecalis. (researchsquare.com)
  • Our findings demonstrate the importance of incorporating multiple strains when determining traits and when performing microbial competition experiments. (lu.se)
  • However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists' understanding of how microbial populations interact to regulate ecosystem processes. (osti.gov)
  • By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortality, and turnover for individual microbial populations within soil assemblages. (osti.gov)
  • This should be reflected in microbial genetic adaption, also indicating which genes are likely important to successfully colonize the human gut. (europa.eu)
  • Thus, research into the fast and complete degradation of BPA, and other compounds via microbial means is of great interest. (rsc.org)
  • A coherent understanding of when mortality of viable microorganisms does or does not occur in dust, and whether different light exposures influence these processes at the microbial community scale, is still lacking. (biomedcentral.com)
  • These molecules can directly serve as nutrients for microbial growth, and depending on the host's immune status, they can determine the outcome of polymicrobial interactions (for example, whether commensals outcompete pathogens or vice versa). (ccf.org)
  • The main achievement of this study is the development of a valuable new technique for investigating biofilm development, including exploring interactions and associations between specific microscopic taxa. (azocleantech.com)
  • The anti-microbial activity of the isolates against Streptococcus mutans associated with caries, and the mucosal pathogens Staphylococcus aureus, Candida albicans and Enterococcus faecalis was determined by determining inhibitory zones on agar plates. (researchsquare.com)
  • In this work, we use isotope incorporation within DNA molecules to model taxon-specific population growth in the presence of 18 O-labeled water. (osti.gov)
  • With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. (frontiersin.org)
  • Some Lactobacillus have also anti-microbial properties. (researchsquare.com)
  • The aim of this study was therefore to identify Lactobacillus isolates from patients with head and neck cancer and to determine their acid-producing capacity and anti-microbial activity. (researchsquare.com)
  • Novel taxa of Firmicutes were discovered, commonly found in warm, slightly alkaline, anoxic fracture fluids. (princeton.edu)