scholarly journals Microbiota differences of the comb jelly Mnemiopsis leidyi in native and invasive sub-populations

2019 ◽  
Author(s):  
Cornelia Jaspers ◽  
Nancy Weiland-Bräuer ◽  
Martin Fischer ◽  
Sven Künzel ◽  
Ruth A. Schmitz ◽  
...  
Keyword(s):  
Amplicon Sequencing ◽  
Sister Group ◽  
Invasion Success ◽  
Mnemiopsis Leidyi ◽  
Rrna Gene ◽  
Indigenous Species ◽  
Controlled Environments ◽  
Non Indigenous Species ◽  
The Impact

ABSTRACTThe translocation of non-indigenous species around the world, especially in marine systems, is a matter of concern for biodiversity conservation and ecosystem functioning. While specific traits are often recognized to influence establishment success of non-indigenous species, the impact of the associated microbial community for the fitness, performance and invasion success of basal marine metazoans remains vastly unknown. In this study we compared the microbiota community composition of the invasive ctenophore Mnemiopsis leidyi in different native and invasive sub-populations along with characterization of the genetic structure of the host. By 16S rRNA gene amplicon sequencing we showed that the sister group to all metazoans, namely ctenophores, harbored a distinct microbiota on the animal host, which significantly differed across two major tissues, namely epidermis and gastrodermis. Additionally, we identified significant differences between native and invasive sub-populations of M. leidyi, which indicate, that the microbiota community is likely influenced by the genotypic background of the ctenophore. To test the hypothesis that the microbiota is genotypically selected for by the ctenophore host, experiments under controlled environments are required.

scholarly journals Development of a robust protocol for the characterization of the pulmonary microbiota

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Nathan Dumont-Leblond ◽  
Marc Veillette ◽  
Christine Racine ◽  
Philippe Joubert ◽  
Caroline Duchaine
Keyword(s):  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Validity Of Results ◽  
Healthy Human ◽  
Bacterial Dna ◽  
Starting Point ◽  
Sampling Procedures ◽  
Negative Controls ◽  
The Impact

AbstractThe lack of methodological standardization diminishes the validity of results obtained and the conclusions drawn when studying the lung microbiota. We report the validation of a complete 16S rRNA gene amplicon sequencing workflow, from patient recruitment to bioinformatics, tailored to the constrains of the pulmonary environment. We minimize the impact of contaminants and establish negative controls to track and account for them at every step. Enzymatic and mechanical homogenization combined to commercially available extraction kits allow for a fast and reliable extraction of bacterial DNA. The DNA extraction kits have a significant impact on the bacterial composition of the controls. The bacterial signatures of extracted cancerous and healthy human tissues from 5 patients are highly distinguishable from methodological controls. Our work expands our understanding of low microbial burdened environments analysis. This article is to be a starting point towards methodological standardization and the implementation of proper sampling procedures in the study of lung microbiota.

scholarly journals Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

2021 ◽  
Author(s):  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Lena Staib ◽  
Etienne V. Doll ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Extraction ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Microbiome Analysis ◽  
Eukaryotic Dna ◽  
Selective Lysis ◽  
The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

scholarly journals Denitrification by benthic foraminifera and their contribution to N-loss from a fjord environment

2021 ◽  
Vol 18 (1) ◽  
pp. 327-341 ◽  
Author(s):  
Constance Choquel ◽  
Emmanuelle Geslin ◽  
Edouard Metzger ◽  
Helena L. Filipsson ◽  
Nils Risgaard-Petersen ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Benthic Foraminifera ◽  
Nitrate Removal ◽  
Nitrate Respiration ◽  
Indigenous Species ◽  
Overlying Water ◽  
Spatial And Temporal Scales ◽  
Chemical Gradients ◽  
Non Indigenous Species ◽  
The Impact

Abstract. Oxygen and nitrate availabilities impact the marine nitrogen cycle at a range of spatial and temporal scales. Here, we demonstrate the impact of denitrifying foraminifera on the nitrogen cycle at two oxygen and nitrate contrasting stations in a fjord environment (Gullmar Fjord, Sweden). Denitrification by benthic foraminifera was determined through the combination of specific density counting per microhabitat and specific nitrate respiration rates obtained through incubation experiments using N2O microsensors. Benthic nitrate removal was calculated from submillimeter chemical gradients extracted from 2D porewater images of the porewater nitrate concentration. These were acquired by combining the DET technique (diffusive equilibrium in thin film) with chemical colorimetry and hyperspectral imagery. Sediments with high nitrate concentrations in the porewater and oxygenated overlying water were dominated by the non-indigenous species (NIS) Nonionella sp. T1. Denitrification by this species could account for 50 %–100 % of the nitrate loss estimated from the nitrate gradients. In contrast sediments below hypoxic bottom waters had low inventories of porewater nitrate, and denitrifying foraminifera were rare. Their contribution to benthic nitrate removal was negligible (< 5 %). Our study showed that benthic foraminifera can be a major contributor to nitrogen mitigation in oxic coastal ecosystems and should be included in ecological and diagenetic models aiming to understand biogeochemical cycles coupled to nitrogen.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

scholarly journals Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12498
Author(s):  
Mauro Maver ◽  
Carmen Escudero-Martinez ◽  
James Abbott ◽  
Jenny Morris ◽  
Pete E. Hedley ◽  
...  
Keyword(s):  
Indole Alkaloid ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Host Genotype ◽  
Independent Manner ◽  
Molecular Determinants ◽  
Breeding Selection ◽  
The Impact ◽  
Soil Interface

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

scholarly journals Characterization of Shallow Whole-Metagenome Shotgun Sequencing as a High-Accuracy and Low-Cost Method by Complicated Mock Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenyi Xu ◽  
Tianda Chen ◽  
Yuwei Pei ◽  
Hao Guo ◽  
Zhuanyu Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Shotgun Sequencing ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Cost Efficient ◽  
Taxonomic Assignments

Characterization of the bacterial composition and functional repertoires of microbiome samples is the most common application of metagenomics. Although deep whole-metagenome shotgun sequencing (WMS) provides high taxonomic resolution, it is generally cost-prohibitive for large longitudinal investigations. Until now, 16S rRNA gene amplicon sequencing (16S) has been the most widely used approach and usually cooperates with WMS to achieve cost-efficiency. However, the accuracy of 16S results and its consistency with WMS data have not been fully elaborated, especially by complicated microbiomes with defined compositional information. Here, we constructed two complex artificial microbiomes, which comprised more than 60 human gut bacterial species with even or varied abundance. Utilizing real fecal samples and mock communities, we provided solid evidence demonstrating that 16S results were of poor consistency with WMS data, and its accuracy was not satisfactory. In contrast, shallow whole-metagenome shotgun sequencing (shallow WMS, S-WMS) with a sequencing depth of 1 Gb provided outputs that highly resembled WMS data at both genus and species levels and presented much higher accuracy taxonomic assignments and functional predictions than 16S, thereby representing a better and cost-efficient alternative to 16S for large-scale microbiome studies.

scholarly journals Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon

2019 ◽  
Vol 7 (8) ◽  
pp. 233 ◽  
Author(s):  
Shruti Gupta ◽  
Jorge Fernandes ◽  
Viswanath Kiron
Keyword(s):  
Atlantic Salmon ◽  
Intestinal Microbiota ◽  
Amplicon Sequencing ◽  
Study Groups ◽  
Oxolinic Acid ◽  
Rrna Gene ◽  
Farmed Fish ◽  
Bacterial Phyla ◽  
Microbial Profile ◽  
The Impact

The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, with potential effects on the host health. In this study, we have elucidated the impact of two antibiotics, florfenicol and oxolinic acid, by employing a high-throughput 16S rRNA gene amplicon sequencing technique on the distal and mid intestinal microbial communities of Atlantic salmon (Salmo salar). For this, Atlantic salmon were offered diets with or without antibiotics. We then investigated the bacterial communities in the intestinal mucus of the fish. Our results showed that antibiotic exposure shifts the intestinal microbial profile differentially. In addition, the bacterial compositions of the control and antibiotic-fed groups were significantly different. Antibiotic feeding altered the composition and abundance of the dominant bacterial phyla, namely Proteobacteria, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes, Tenericutes, and Thermotogae. The bacterial association network analysis also indicated the differential pattern of co-occurrence of bacteria in the three study groups. The results regarding the differences in the structure and association of the intestinal microbiota of Atlantic salmon after florfenicol and oxolinic acid feeding can be employed to attenuate the adverse effects of antibiotic feeding on fish.

scholarly journals Effect of Salinity on the Gut Microbiome of Pike Fry (Esox lucius)

2020 ◽  
Vol 10 (7) ◽  
pp. 2506
Author(s):  
Tomasz Dulski ◽  
Roman Kujawa ◽  
Martyna Godzieba ◽  
Slawomir Ciesielski
Keyword(s):  
Gut Microbiome ◽  
High Salinity ◽  
Fish Farming ◽  
Amplicon Sequencing ◽  
Good Alternative ◽  
Control Group ◽  
Rrna Gene ◽  
Microbiological Analysis ◽  
Early Life Stages ◽  
The Impact

The increasing popularity of pike in angling and fish farming has created a need to increase pike production. However, intensive pike farming is subject to limitations due to diseases and pathogens. Sodium chloride (NaCl) could be a good alternative to chemotherapeutics, especially for protecting the fish against pathogens and parasites at early life stages. However, the impact of high salinity on the symbiotic bacteria inhabiting freshwater fish is still unclear. Therefore, our objective was to analyze the gut microbiome to find possible changes caused by salinity. In this study, the influence of 3‰ and 7‰ salinity on pike fry was investigated. High-throughput 16S rRNA gene amplicon sequencing was used to profile the gut microbiome of the fish. It was found that salinity had a statistically significant influence on pike fry mortality. Mortality was highest in the 7‰ salinity group and lowest in the 3‰ group. Microbiological analysis indicated that Proteobacteria and Actinobacteria predominated in the pike gut microbiome in all examined groups, followed by lower percentages of Bacteroidetes and Firmicutes. There were no statistically significant differences in the percent abundance of bacterial taxa between the control group and groups with a higher salinity. Our results suggest that salinity influences the gut microbiome structure in pike fry, and that 3‰ salinity may be a good solution for culturing pike at this stage in their development.

scholarly journals Half-Elemental Diet Shifts the Human Intestinal Bacterial Compositions and Metabolites: A Pilot Study with Healthy Individuals

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Jun Miyoshi ◽  
Daisuke Saito ◽  
Mio Nakamura ◽  
Miki Miura ◽  
Tatsuya Mitsui ◽  
...  
Keyword(s):  
Pilot Study ◽  
Gut Microbiota ◽  
Dietary Habits ◽  
Elemental Diet ◽  
Amplicon Sequencing ◽  
Short Chain Fatty Acids ◽  
Rrna Gene ◽  
Healthy Individuals ◽  
The Impact ◽  
Time Point

Background and Aim. Half-elemental diet (ED) (900 kcal/day of ED) has clinical efficacy to treat Crohn’s disease (CD). However, the underlying mechanisms of how the ED exerts its efficacy remain unclear. Alterations of the gut microbiota, known as dysbiosis, have been reported to play a role in CD pathogenesis. Many variables including diet affect the gut microbiota. We hypothesized that half-ED has the potential to change the gut microbiota composition and functions leading to anti-inflammatory actions. Given that inflammation can be a confounding factor affecting the intestinal microbiota, we aimed to test our hypothesis among healthy individuals in this pilot study. Methods. This prospective study included four healthy volunteers. The subjects continued their dietary habits for 2 weeks after the registration of the study and then started half-ED replacing 900 kcal of the regular diet with ED (time point 1, T1). The subjects continued half-ED for 2 weeks (T2). After the withdrawal of ED, subjects resumed their original dietary habits for 2 weeks (T3). Fecal samples were collected from all subjects at all time points, T1-3. Fecal DNA and metabolites were extracted from the samples. We performed 16S rRNA gene amplicon sequencing and metabolomic analysis to examine the bacterial compositions and intestinal metabolites. Results. There were differences in the gut bacterial compositions and metabolites at each time point as well as overtime changing patterns between subjects. Several bacteria and metabolites including short-chain fatty acids and bile acids altered significantly across the subjects. The bacterial membership and intestinal metabolites at T3 were different from T1 in all subjects. Conclusions. Half-ED shifts the gut bacterial compositions and metabolites. The changes varied with each individual, while some microbes and metabolites change commonly across individuals. The impact of half-ED may persist even after the withdrawal. This trial is registered with UMIN ID: 000031920.

scholarly journals Hill-based dissimilarity indices and null models for analysis of microbial community assembly

2020 ◽  
Author(s):  
Oskar Modin ◽  
Raquel Liébana ◽  
Soroush Sabeh-Alam ◽  
Britt-Marie Wilén ◽  
Carolina Suarez ◽  
...  
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Community Assembly ◽  
Null Model ◽  
Amplicon Sequencing ◽  
Marker Genes ◽  
Rrna Gene ◽  
Data Set ◽  
Microbial Community Assembly ◽  
The Impact

Abstract Background: High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.Results: Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choices of bioinformatics pipeline and dissimilarity index can have considerable impacts on results and conclusions. Analysis of the AGS data set showed that results are sensitive to bioinformatics choices when dissimilarities between sample groups are compared with incidence-based indices. Analysis of the MFC data set with a combination of Hill-based indices and a null model revealed that random dispersal could explain the distribution of both rare and highly abundant taxa within a glucose-fed MFC whereas the distribution of taxa of intermediate relative abundance was governed by heterogeneous selection.Conclusions: Hill-based indices provides a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic factors on taxa of low-, intermediate-, and high relative abundance during microbial community assembly can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv).

Sign in / Sign up

Export Citation Format

Share Document