scholarly journals The piglet mycobiome during the weaning transition: a pilot study1

2019 ◽  
Vol 97 (7) ◽  
pp. 2889-2900 ◽  
Author(s):  
Katie L Summers ◽  
Juli Foster Frey ◽  
Timothy G Ramsay ◽  
Ann M Arfken
Keyword(s):  
Pilot Study ◽  
High Throughput Sequencing ◽  
Temporal Dynamics ◽  
Bacterial Species ◽  
Bacterial Populations ◽  
Point Of Interest ◽  
Host Health ◽  
Culturable Fungi ◽  
Culture Independent ◽  
Fungal Populations

Abstract The importance of the microbiota in the gastrointestinal tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this pilot study, we sought to assess and characterize the mycobiome in the feces of swine from birth through the critical weaning transition to investigate the mycobiome population and its temporal dynamics in piglet feces. Cultured fecal samples demonstrate a significant increase in fungal burden following weaning that does not differ from adult levels, suggesting stable colonization. Culturable fungi were not found in any environmental samples tested, including water, food, sow milk or colostrum. To determine the fungal diversity present and to address the problem of unculturable fungi, we performed a pilot study utilizing ITS and 16S rRNA focused primers for high-throughput sequencing of fungal and bacterial species, respectively. Bacterial populations increase in diversity over the experimental timeline (days 1 to 35 postbirth), but the fungal populations do not demonstrate the same temporal trend. Following weaning, there is a dynamic shift in the feces to a Saccharomycetaceae-dominated population. The shift in fungal population was because of the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal gastrointestinal tracts. This study provides insights into the early colonization and subsequent establishment of fungi during the weaning transition in piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition.

scholarly journals 176 Characterizing the mycobiome in piglets during the weaning transition

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 177-177
Author(s):  
Ann Arfken ◽  
Juli Frey ◽  
Timothy Ramsay ◽  
Katie L Summers
Keyword(s):  
Gi Tract ◽  
Fatty Acid Production ◽  
Bacterial Populations ◽  
Fiber Degradation ◽  
Host Health ◽  
Culture Independent ◽  
Fungal Organisms ◽  
Fungal Populations ◽  
High Degree ◽  
Slow Growing

Abstract The importance of the microbiota in the gastrointestinal (GI) tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time of interest to industry. In this study, we sought to assess and characterize the mycobiome and microbiome in the feces and GI tract of swine from birth through the critical weaning transition (days 1–35 post-birth). In addition, we investigated environmental factors that may alter microorganisms present in piglets. Fecal bacterial populations increased in diversity over the experimental timeline and demonstrated a transition from an Enterobacteriaceae-dominated population, to a Prevotellaceae and Ruminococcaceae-dominated population by days 24–35 post-birth. These later populations are capable of fiber degradation and short chain fatty acid production. In fecal fungal populations, richness and diversity peaked at weaning and declined post-weaning. There was also a dynamic shift in the mycobiome to a Saccharomycetaceae-dominated population that remained stable into adulthood. Fungal organisms contributing to this colonization were not found in environmental samples including water, colostrum, and feed. Despite fungal populations present in the feces of sows, these maternal fungi were not similar to the piglet mycobiome and thus did not indicate a maternally-derived effect. Furthermore, the microbiomes of the GI tract showed decreased richness and diversity in the upper GI compared to the lower GI, and a high degree of individual variation and litter effect throughout the organs. This study provides insights into the early colonization and establishment of fungi during the weaning transition. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition, including their role in fast- versus slow-growing piglets.

scholarly journals Human gut microbiota and future prebiotics

2012 ◽  
Vol 33 (3) ◽  
pp. 100
Author(s):  
Michael Conlon ◽  
Anthony Bird ◽  
Claus Christohersen
Keyword(s):  
Gut Microbiota ◽  
Human Gastrointestinal Tract ◽  
Human Gut ◽  
Bacterial Populations ◽  
Independent Analysis ◽  
Host Health ◽  
Culture Independent ◽  
The Status ◽  
Diet And Lifestyle ◽  
Contemporary Approach

Rapid advances in molecular methods that enable culture-independent analysis of the complex bacterial populations is increasing awareness and understanding of the composition and activity of the microbiota in the human gastrointestinal tract, its role in host health and response to changes in diet and lifestyle. In this article we discuss the shortcomings of the contemporary approach of targeting a few selected bacteria, notably lactobacilli and bifidobacteria, to gauge the status of the gut microbiota for promoting health of the human host.

scholarly journals Impact of lignans in oilseed mix on gut microbiome composition and enterolignan production in younger healthy and premenopausal women: an in vitro pilot study

2020 ◽  
Author(s):  
GIULIA CORONA ◽  
Anna Kreimes ◽  
Monica Barone ◽  
Silvia Turroni ◽  
PATRIZIA BRIGIDI ◽  
...  
Keyword(s):  
Pilot Study ◽  
Gut Microbiota ◽  
Batch Culture ◽  
Temporal Dynamics ◽  
Bacterial Species ◽  
Premenopausal Women ◽  
Small Sample ◽  
Rrna Gene ◽  
Faecal Samples

Abstract Background: Dietary lignans belong to the group of phytoestrogens together with coumestans, stilbenes and isoflavones, and themselves do not exhibit oestrogen-like properties. Nonetheless, the gut microbiota converts them into enterolignans, which show chemical similarity to the human oestrogen molecule. One of the richest dietary sources of lignans are oilseeds, including flaxseed. The aim of this pilot study was to determine the concentration of the main dietary lignans in an oilseed mix, and explore the gut microbiota-dependent production of enterolignans for oestrogen substitution in young and premenopausal women. The oilseed mix was fermented in a pH-controlled batch culture system inoculated with women’s faecal samples. The lignan content and enterolignan production were measured by ultra‐high-performance liquid chromatography – tandem mass spectrometry (UHPLC-MS/MS), and the faecal-derived microbial communities were profiled by 16S rRNA gene-based next-generation sequencing. Results: In vitro batch culture fermentation of faecal samples inoculated with oilseed mix for 24 h resulted in a substantial increase in enterolactone production in younger women and an increase in enterodiol in the premenopausal group. As for the gut microbiota, different baseline profiles were observed as well as different temporal dynamics, mainly related to Clostridiaceae , and Klebsiella and Collinsella spp. Conclusions: Despite the small sample size, our pilot study revealed that lignan-rich oilseeds could strongly influence the faecal microbiota of both younger and premenopausal females, leading to a different enterolignan profile being produced. Further studies in larger cohorts are needed to evaluate the long-term effects of lignan-rich diets on the gut microbiota and find out how enterolactone-producing bacterial species could be increased. Diets rich in lignans could potentially serve as a safe supplement of oestrogen analogues to meet the cellular needs of endogenous oestrogen and deliver numerous health benefits, provided that the premenopausal woman microbiota is capable of converting dietary precursors into enterolignans.

Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Akshatha Prasanna ◽  
Vidya Niranjan
Keyword(s):  
Antimicrobial Resistance ◽  
High Performance ◽  
Pathogen Detection ◽  
Bacterial Species ◽  
Workflow Management ◽  
Metagenomic Data ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent ◽  
Automated Pipeline ◽  
User Friendly

Background: Since bacteria are the earliest known organisms, there has been significant interest in their variety and biology, most certainly concerning human health. Recent advances in Metagenomics sequencing (mNGS), a culture-independent sequencing technology have facilitated an accelerated development in clinical microbiology and our understanding of pathogens. Objective: For the implementation of mNGS in routine clinical practice to become feasible, a practical and scalable strategy for the study of mNGS data is essential. This study presents a robust automated pipeline to analyze clinical metagenomic data for pathogen identification and classification. Method: The proposed Clin-mNGS pipeline is an integrated, open-source, scalable, reproducible, and user-friendly framework scripted using the Snakemake workflow management software. The implementation avoids the hassle of manual installation and configuration of the multiple command-line tools and dependencies. The approach directly screens pathogens from clinical raw reads and generates consolidated reports for each sample. Results: The pipeline is demonstrated using publicly available data and is tested on a desktop Linux system and a High-performance cluster. The study compares variability in results from different tools and versions. The versions of the tools are made user modifiable. The pipeline results in quality check, filtered reads, host subtraction, assembled contigs, assembly metrics, relative abundances of bacterial species, antimicrobial resistance genes, plasmid finding, and virulence factors identification. The results obtained from the pipeline are evaluated based on sensitivity and positive predictive value. Conclusion: Clin-mNGS is an automated Snakemake pipeline validated for the analysis of microbial clinical metagenomics reads to perform taxonomic classification and antimicrobial resistance prediction.

scholarly journals Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson
Keyword(s):  
Community Composition ◽  
Environmental Effects ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Species Identity ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Culture Independent ◽  
The Impact ◽  
Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut

mBio ◽  
2014 ◽  
Vol 5 (6) ◽  
Author(s):  
Matthew Jemielita ◽  
Michael J. Taormina ◽  
Adam R. Burns ◽  
Jennifer S. Hampton ◽  
Annah S. Rolig ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Spatial Structure ◽  
Growth Kinetics ◽  
Spatial Organization ◽  
Temporal Dynamics ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Light Sheet ◽  
Logistic Growth ◽  
Light Sheet Fluorescence Microscopy

ABSTRACTThe vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of anAeromonasspecies, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly.IMPORTANCEOur intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging.

scholarly journals Culture-independent pilot study of microbiota colonizing open fractures and association with severity, mechanism, location, and complication from presentation to early outpatient follow-up

2014 ◽  
Vol 32 (4) ◽  
pp. 597-605 ◽  
Author(s):  
Geoffrey D. Hannigan ◽  
Brendan P. Hodkinson ◽  
Kelly McGinnis ◽  
Amanda S. Tyldsley ◽  
Jason B. Anari ◽  
...  
Keyword(s):  
Pilot Study ◽  
Open Fractures ◽  
Culture Independent

Effects of potassium azide on soil microbial populations and soil enzymatic activities

1975 ◽  
Vol 21 (4) ◽  
pp. 565-570 ◽  
Author(s):  
W. D. Kelley ◽  
R. Rodriguez-Kabana
Keyword(s):  
Soil Enzyme ◽  
Soil Microflora ◽  
Microbial Populations ◽  
Bacterial Populations ◽  
Soil Microbial ◽  
Fungal Populations ◽  
Potassium Azide ◽  
Time Changes ◽  
Bacteria And Fungi ◽  
Microbial Numbers

Preplant applications of potassium azide (KN3) to pine nursery beds were evaluated for effect on the soil microflora and on soil enzyme activity where either plastic-sealing or water-sealing techniques were used. Two weeks after incorporation of azide (0–224 kg/ha), soil samplings revealed reduced populations of bacteria and fungi and a corresponding decline in invertase and amylase activities. These effects were proportionate to the amount of azide used and were more pronounced in plastic-sealed plots. Phosphatase activity was little affected. Five weeks after azide application, bacterial populations were higher in treated plots than in controls. Greater numbers of bacteria were recorded from plastic-sealed plots and highest populations coincided with plots receiving the highest rates of azide, regardless of the sealing technique. Fungal populations at this sampling were generally less in treated plots than in the controls, but were higher under plastic seal. At this time, changes in invertase and amylase activities did not correspond to increased microbial numbers. Sixteen weeks after applications of KN3, bacterial populations in treated plots did not differ significantly from controls, but remained higher in plastic-sealed than water-sealed plots. Fungal populations under plastic seal had changed little and remained significantly lower in treated water-sealed plots than in controls. The earlier recorded reduction in invertase and amylase activities was still evident at the final sampling.

Ice nucleation activity of bacteria isolated from snow compared with organic and inorganic substrates

2008 ◽  
Vol 5 (6) ◽  
pp. 373 ◽  
Author(s):  
Roya Mortazavi ◽  
Christopher T. Hayes ◽  
Parisa A. Ariya
Keyword(s):  
Bacterial Species ◽  
Ice Nucleation ◽  
Detailed Knowledge ◽  
Bacterial Populations ◽  
Inorganic Aerosols ◽  
Ice Nucleators ◽  
Species Population ◽  
Nucleation Activity ◽  
Ice Nucleation Activity ◽  
Snow Samples

Environmental context. Biological ice nucleators have been found to freeze water at very warm temperatures. The potential of bio-aerosols to greatly influence cloud chemistry and microphysics is becoming increasingly apparent, yet detailed knowledge of their actual role in atmospheric processes is lacking. The formation of ice in the atmosphere has significant local, regional and global influence, ranging from precipitation to cloud nucleation and thus climate. Ice nucleation tests on bacteria isolated from snow and laboratory-grown bacteria, in comparison with those of known organic and inorganic aerosols, shed light on this issue. Abstract. Ice nucleation experiments on bacteria isolated from snow as well as grown in the laboratory, in comparison with those of known organic and inorganic aerosols, examined the importance of bio-aerosols on cloud processes. Snow samples were collected from urban and suburban sites in the greater Montreal region in Canada (45°28′N, 73°45′W). Among many snow bacterial isolates, eight types of bacterial species, none belonging to known effective ice nucleators such as Pseudomonas or Erwinia genera, were identified to show an intermediate range of ice nucleation activity (–12.9 ± 1.3°C to –17.5 ± 2.8°C). Comparable results were also obtained for molten snow samples and inorganic suspensions (kaolin and montmorillonite) of buffered water solutions. The presence of organic molecules (oxalic, malonic and succinic acids) had minimal effect (<2°C) on ice nucleation. Considering experimental limitations, and drawing from observation in snow samples of a variety of bacterial populations with variable ice-nucleation ability, a shift in airborne-species population may significantly alter glaciation processes in clouds.

Sign in / Sign up

Export Citation Format

Share Document