scholarly journals The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1612 ◽  
Author(s):  
Zachery T. Lewis ◽  
Jasmine C.C. Davis ◽  
Jennifer T. Smilowitz ◽  
J. Bruce German ◽  
Carlito B. Lebrilla ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Freeze Drying ◽  
Marker Gene ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Sample Treatment ◽  
Sequencing Data ◽  
Fecal Samples ◽  
Freeze Dried ◽  
The Impact

Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation ofBacteriodesand a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.

scholarly journals A critical perspective on interpreting amplicon sequencing data in soil ecological research

2021 ◽  
Author(s):  
Lauren V. Alteio ◽  
Joana Séneca ◽  
Alberto Canarini ◽  
Roey Angel ◽  
Ksenia Guseva ◽  
...  
Keyword(s):  
Statistical Power ◽  
Marker Gene ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Data Availability ◽  
Microbial Community Analysis ◽  
Sequencing Data ◽  
Spatio Temporal ◽  
Complementary Techniques ◽  
The Impact

Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing studies in soil and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation and availability to improve the rigor of future studies.

scholarly journals Effect of Freeze Drying and Simulated Gastrointestinal Digestion on Phenolic Metabolites and Antioxidant Property of the Natal Plum (Carissa macrocarpa)

Foods ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1420
Author(s):  
Faith Seke ◽  
Vimbainashe E. Manhivi ◽  
Tinotenda Shoko ◽  
Retha M. Slabbert ◽  
Yasmina Sultanbawa ◽  
...  
Keyword(s):  
Freeze Drying ◽  
Array Detector ◽  
Gastrointestinal Digestion ◽  
Liquid Chromatograph ◽  
Antioxidant Power ◽  
Intestinal Phase ◽  
Glucosidase Activity ◽  
Freeze Dried ◽  
Small Intestinal ◽  
The Impact

Natal plums (Carissa macrocarpa) are a natural source of bioactive compounds, particularly anthocyanins, and can be consumed as a snack. This study characterized the impact of freeze drying and in vitro gastrointestinal digestion on the phenolic profile, antioxidant capacity, and α-glucosidase activity of the Natal plum (Carissa macrocarpa). The phenolic compounds were quantified using high performance liquid chromatography coupled to a diode-array detector HPLC-DAD and an ultra-performance liquid chromatograph (UPLC) with a Waters Acquity photodiode array detector (PDA) coupled to a Synapt G2 quadrupole time-of-flight (QTOF) mass spectrometer. Cyanidin-3-O-β-sambubioside (Cy-3-Sa) and cyanidin-3-O-glucoside (Cy-3-G) were the dominant anthocyanins in the fresh and freeze-dried Natal plum powder. Freeze drying did not affect the concentrations of both cyanidin compounds compared to the fresh fruit. Both cyanidin compounds, ellagic acid, catechin, epicatechin syringic acid, caffeic acid, luteolin, and quercetin O-glycoside from the ingested freeze-dried Natal plum powder was quite stable in the gastric phase compared to the small intestinal phase. Cyanidin-3-O-β-sambubioside from the ingested Natal plum powder showed bioaccessibility of 32.2% compared to cyanidin-3-O-glucoside (16.3%). The degradation of anthocyanins increased the bioaccessibility of gallic acid, protocatechuic acid, coumaric acid, and ferulic acid significantly, in the small intestinal digesta. The ferric reducing antioxidant power (FRAP), 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) activities, and inhibitory effect of α-glucosidase activity decreased in the small intestinal phase. Indigenous fruits or freeze-dried powders with Cy-3-Sa can be a better source of anthocyanin than Cy-3-G due to higher bioaccessibility in the small intestinal phase.

Tu1716 Evaluation of the Impact of Different Commercially Available DNA Extraction Kits and Laboratories for Assessing Bacterial Community Structure in Fecal Samples - Implications for IBD Research

2013 ◽  
Vol 144 (5) ◽  
pp. S-829
Author(s):  
Nicholas A. Kennedy ◽  
Alan Walker ◽  
UK IBD Microbiota Consortia ◽  
UK IBD Genetics Consortia ◽  
Susan H. Berry ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Dna Extraction ◽  
Bacterial Community Structure ◽  
Fecal Samples ◽  
The Impact

scholarly journals Studies on the Catalytic Properties of Crude Freeze-Dried Preparations of Yarrowia lipolytica Extracellular Lipases for Geranyl Ester Derivative Synthesis

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 839
Author(s):  
Karina Jasińska ◽  
Bartłomiej Zieniuk ◽  
Dorota Nowak ◽  
Agata Fabiszewska
Keyword(s):  
Freeze Drying ◽  
Antioxidant Properties ◽  
Antibacterial Properties ◽  
Synthetic Activity ◽  
Drying Process ◽  
Enzyme Preparations ◽  
Ester Derivative ◽  
Freeze Dried ◽  
The Impact ◽  
Geranyl Ester

The study aimed to evaluate the impact of selected factors of the freeze-drying process on the hydrolytic and synthetic activity of the extracellular lipases of Y. lipolytica KKP 379 and to attempt the use of the crude enzyme preparation as a biocatalyst in the synthesis of geranyl 4-hydroxyphenylpropanoate. Antioxidant and antibacterial properties of the geranyl ester derivative were also investigated in order to evaluate their usefulness as a novel food additive. The studies confirmed that freeze-drying was an effective method of dehydrating yeast supernatant and allowed for obtaining lyophilizates with low water activity from 0.055 to 0.160. The type and concentration of the additive (2–6% whey protein hydrolyzate, 0.5% and 1% ammonium sulphate) had a significant effect on the hydrolytic activity of enzyme preparations, while the selected variants of drying temperature during the freeze-drying process were not significant (10 °C and 50 °C). Low yield of geranyl 4-hydroxyphenylopropionate was shown when the lyophilized supernatant was used (5.3%), but the yield of ester synthesis increased when the freeze-dried Y. lipolytica yeast biomass was applied (47.9%). The study confirmed the antioxidant properties of the synthesized ester by the DPPH• and CUPRAC methods, as well as higher antibacterial activity against tested bacteria than its precursor with 0.125 mM MIC (minimal inhibitory concentration) against L. monocytogenes.

scholarly journals Efficient phasing and imputation of low-coverage sequencing data using large reference panels

2020 ◽  
Author(s):  
S. Rubinacci ◽  
D.M. Ribeiro ◽  
R. Hofmeister ◽  
O. Delaneau
Keyword(s):  
Paradigm Shift ◽  
Rare Variants ◽  
Association Studies ◽  
Cost Effective ◽  
Human Populations ◽  
Sequencing Data ◽  
Snp Arrays ◽  
Genomic Studies ◽  
Low Coverage ◽  
The Impact

AbstractLow-coverage whole genome sequencing followed by imputation has been proposed as a cost-effective genotyping approach for disease and population genetics studies. However, its competitiveness against SNP arrays is undermined as current imputation methods are computationally expensive and unable to leverage large reference panels.Here, we describe a method, GLIMPSE, for phasing and imputation of low-coverage sequencing datasets from modern reference panels. We demonstrate its remarkable performance across different coverages and human populations. It achieves imputation of a full genome for less than $1, outperforming existing methods by orders of magnitude, with an increased accuracy of more than 20% at rare variants. We also show that 1x coverage enables effective association studies and is better suited than dense SNP arrays to access the impact of rare variations. Overall, this study demonstrates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.

scholarly journals Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Paul E. Smith ◽  
Sinead M. Waters ◽  
Ruth Gómez Expósito ◽  
Hauke Smidt ◽  
Ciara A. Carberry ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Gas Production ◽  
Reference Database ◽  
Specific Reference ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
Rumen Microbiota ◽  
Reference Databases

Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies. Indeed, with the use of barcoded amplicon sequencing, it is now cost effective and computationally feasible to identify individual rumen microbial genera associated with ruminant livestock nutrition, genetics, performance and greenhouse gas production. However, across all disciplines of microbial ecology, there is currently little reporting of the use of internal controls for validating HTS results. Furthermore, there is little consensus of the most appropriate reference database for analyzing rumen microbiota amplicon sequencing data. Therefore, in this study, a synthetic rumen-specific sequencing standard was used to assess the effects of database choice on results obtained from rumen microbial amplicon sequencing. Four DADA2 reference training sets (RDP, SILVA, GTDB, and RefSeq + RDP) were compared to assess their ability to correctly classify sequences included in the rumen-specific sequencing standard. In addition, two thresholds of phylogenetic bootstrapping, 50 and 80, were applied to investigate the effect of increasing stringency. Sequence classification differences were apparent amongst the databases. For example the classification of Clostridium differed between all databases, thus highlighting the need for a consistent approach to nomenclature amongst different reference databases. It is hoped the effect of database on taxonomic classification observed in this study, will encourage research groups across various microbial disciplines to develop and routinely use their own microbiome-specific reference standard to validate analysis pipelines and database choice.

scholarly journals To rarefy or not to rarefy: Enhancing microbial community analysis through next-generation sequencing

2020 ◽  
Author(s):  
Ellen S. Cameron ◽  
Philip J. Schmidt ◽  
Benjamin J.-M. Tremblay ◽  
Monica B. Emelko ◽  
Kirsten M. Müller
Keyword(s):  
Microbial Community ◽  
Community Analysis ◽  
Amplicon Sequencing ◽  
Microbial Community Analysis ◽  
List Type ◽  
Sequencing Data ◽  
Water And Wastewater Treatment ◽  
Library Size ◽  
Size Selection ◽  
The Impact

AbstractThe application of amplicon sequencing in water research provides a rapid and sensitive technique for microbial community analysis in a variety of environments ranging from freshwater lakes to water and wastewater treatment plants. It has revolutionized our ability to study DNA collected from environmental samples by eliminating the challenges associated with lab cultivation and taxonomic identification. DNA sequencing data consist of discrete counts of sequence reads, the total number of which is the library size. Samples may have different library sizes and thus, a normalization technique is required to meaningfully compare them. The process of randomly subsampling sequences to a selected normalized library size from the sample library—rarefying—is one such normalization technique. However, rarefying has been criticized as a normalization technique because data can be omitted through the exclusion of either excess sequences or entire samples, depending on the rarefied library size selected. Although it has been suggested that rarefying should be avoided altogether, we propose that repeatedly rarefying enables (i) characterization of the variation introduced to diversity analyses by this random subsampling and (ii) selection of smaller library sizes where necessary to incorporate all samples in the analysis. Rarefying may be a statistically valid normalization technique, but researchers should evaluate their data to make appropriate decisions regarding library size selection and subsampling type. The impact of normalized library size selection and rarefying with or without replacement in diversity analyses were evaluated herein.Highlights▪ Amplicon sequencing technology for environmental water samples is reviewed▪ Sequencing data must be normalized to allow comparison in diversity analyses▪ Rarefying normalizes library sizes by subsampling from observed sequences▪ Criticisms of data loss through rarefying can be resolved by rarefying repeatedly▪ Rarefying repeatedly characterizes errors introduced by subsampling sequences

scholarly journals Study of vacuum and freeze drying of bee honey

2020 ◽  
Vol 24 (6 Part B) ◽  
pp. 4241-4251
Author(s):  
Nebojsa Nedic ◽  
Milan Gojak ◽  
Ivan Zlatanovic ◽  
Nedzad Rudonja ◽  
Kristina Lazarevic ◽  
...  
Keyword(s):  
Water Activity ◽  
High Performance ◽  
Freeze Drying ◽  
Soluble Solids ◽  
Diffusivity Coefficient ◽  
Chromatography Method ◽  
Drying Time ◽  
Freeze Dried ◽  
Acacia Honey ◽  
The Impact

The aim of this research is to study the drying kinetics of vacuum-dried and freeze-dried bee honey produced from two different varieties: Sunflower honey (Helianthus Annuus L.) and Acacia honey (Robinia pseudo acacia L.). Vacuum drying treatments were carried out with the honey samples? initial temperatures of +25?C, ?20?C, and ?40?C. Water content, total soluble solids, as well as the water activity of fresh and dried honey samples were determined. Freeze-drying of bee honey with initial sample temperature of ?40?C has resulted in shorter drying time (7-9 hours), moisture content (10%-12%), water activity (0.405-0.427 aW) and effective moisture diffusivity coefficient (8.26?10?7-9.51?10-7 m2/s). The high-performance liquid chromatography method was used when analyzing the impact that drying pre-treatments had on honey quality. The application of pre-treatments has led to an increase in hydroxy-methyl-furfural by 39-71%, and a decrease in diastase activity by 17-36%, all compared to fresh honey samples. The solutions of Verma model proved to be the best fit with the experimental results.

scholarly journals Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10302
Author(s):  
Li Song ◽  
Zhenzhi Pan ◽  
Yi Dai ◽  
Lin Chen ◽  
Li Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Cadmium Concentration ◽  
Normal Growth ◽  
Amplicon Sequencing ◽  
Negative Influence ◽  
Cadmium Pollution ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

Sign in / Sign up

Export Citation Format

Share Document