scholarly journals Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets

2019 ◽  
Vol 7 (9) ◽  
pp. 343 ◽  
Author(s):  
Gresse ◽  
Chaucheyras Durand ◽  
Dunière ◽  
Blanquet-Diot ◽  
Forano
Keyword(s):  
Microbial Communities ◽  
Digestive Tract ◽  
High Throughput Sequencing ◽  
Archaeal Community ◽  
Short Chain Fatty Acids ◽  
Structural Level ◽  
Additional Information ◽  
Functional Profiling ◽  
Enteric Infections ◽  
Weaning Piglets

Dietary, environmental, and social stresses induced by weaning transition in pig production are associated with alterations of gut microbiota, diarrhea, and enteric infections. With the boom of -omic technologies, numerous studies have investigated the dynamics of fecal bacterial communities of piglets throughout weaning but much less research has been focused on the composition and functional properties of microbial communities inhabiting other gastrointestinal segments. The objective of the present study was to bring additional information about the piglet bacterial and archaeal microbiota throughout the entire digestive tract, both at the structural level by using quantitative PCR and high-throughput sequencing, and on functionality by measurement of short-chain fatty acids and predictions using Tax4Fun tool. Our results highlighted strong structural and functional differences between microbial communities inhabiting the fore and the lower gut as well as a quantitatively important archaeal community in the hindgut. The presence of opportunistic pathogens was also noticed throughout the entire digestive tract and could trigger infection emergence. Understanding the role of the intestinal piglet microbiota at weaning could provide further information about the etiology of post-weaning infections and lead to the development of effective preventive solutions.

scholarly journals Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ya Wang ◽  
Yan Yan ◽  
Kelsey N. Thompson ◽  
Sena Bae ◽  
Emma K. Accorsi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Comprehensive Evaluation ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Rrna Gene ◽  
Propidium Monoazide ◽  
Functional Profiling ◽  
Subway System ◽  
Compositional Diversity

Abstract Background High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples.

scholarly journals Planktonic Bacterial and Archaeal Communities in an Artificially Irrigated Estuarine Wetland: Diversity, Distribution, and Responses to Environmental Parameters

2020 ◽  
Vol 8 (2) ◽  
pp. 198
Author(s):  
Mingyue Li ◽  
Tiezhu Mi ◽  
Zhigang Yu ◽  
Manman Ma ◽  
Yu Zhen
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Archaeal Community ◽  
Rrna Gene ◽  
Liaohe River ◽  
Estuarine Wetland ◽  
Bacterial And Archaeal Communities ◽  
Archaeal Communities

Bacterial and archaeal communities play important roles in wetland ecosystems. Although the microbial communities in the soils and sediments of wetlands have been studied extensively, the comprehensive distributions of planktonic bacterial and archaeal communities and their responses to environmental variables in wetlands remain poorly understood. The present study investigated the spatiotemporal characteristics of the bacterial and archaeal communities in the water of an artificially irrigated estuarine wetland of the Liaohe River, China, explored whether the wetland effluent changed the bacterial and archaeal communities in the Liaohe River, and evaluated the driving environmental factors. Within the study, 16S rRNA quantitative PCR methods and MiSeq high-throughput sequencing were used. The bacterial and archaeal 16S rRNA gene abundances showed significant temporal variation. Meanwhile, the bacterial and archaeal structures showed temporal but not spatial variation in the wetland and did not change in the Liaohe River after wetland drainage. Moreover, the bacterial communities tended to have higher diversity in the wetland water in summer and in the scarce zone, while a relatively higher diversity of archaeal communities was found in autumn and in the intensive zone. DO, pH and PO4-P were proven to be the essential environmental parameters shaping the planktonic bacterial and archaeal community structures in the Liaohe River estuarine wetland (LEW). The LEW had a high potential for methanogenesis, which could be reflected by the composition of the microbial communities.

scholarly journals Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

2020 ◽  
Author(s):  
Ya Wang ◽  
Yan Yan ◽  
Kelsey N. Thompson ◽  
Sena Bae ◽  
Emma K. Accorsi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Comprehensive Evaluation ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Rrna Gene ◽  
Propidium Monoazide ◽  
Functional Profiling ◽  
Subway System ◽  
Compositional Diversity

Abstract Background High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g. qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA-responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities, but provided only qualitative assessments in realistically complex community samples.

scholarly journals The signal and the noise - characteristics of antisense RNA in complex microbial communities

2019 ◽  
Author(s):  
Thomas Yssing Michaelsen ◽  
Jakob Brandt ◽  
Caitlin Singleton ◽  
Rasmus Hansen Kirkegaard ◽  
Nicola Segata ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Antisense Rna ◽  
High Throughput Sequencing ◽  
Antisense Transcription ◽  
Individual Species ◽  
List Type ◽  
Additional Information ◽  
Noise Characteristics ◽  
Insight Into

AbstractHigh-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With the onset of metatranscriptomics, it is now possible to interrogate the transcriptome of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic datasets contain a rich suite of additional information which is just beginning to be explored. In this minireview we discuss the different computational strategies for handling antisense expression in metatranscriptomic samples and highlight their potentially detrimental effects on downstream analysis and interpretation. We also surveyed the antisense transcriptome of multiple genomes and metagenome-assembled genomes (MAGs) from five different datasets and found high variability in the level of antisense transcription for individual species which were consistent across samples. Importantly, we tested the hypothesis that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from a compounded effect of both random, biological and technical factors. Antisense transcription can provide a rich set of information, from technical details about data quality to novel insight into the biology of complex microbial communities.Key pointsSeveral fundamentally different approaches are used to handle antisense RNAPrevalence of antisense RNA is highly variable between communities, genomes, and genes.Antisense RNA is likely an opaque mixture of technical, biological and random effects

scholarly journals Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

2020 ◽  
Author(s):  
Ya Wang ◽  
Yan Yan ◽  
Kelsey N. Thompson ◽  
Sena Bae ◽  
Emma K. Accorsi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Comprehensive Evaluation ◽  
Amplicon Sequencing ◽  
Human Saliva ◽  
Rrna Gene ◽  
Propidium Monoazide ◽  
Functional Profiling ◽  
Subway System ◽  
Compositional Diversity

Abstract Background: High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g. qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting “viable” communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark “PMA-seq” (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. Results: PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis . However, in realistically complex communities (computer screens, computer mice, soil and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability, with its performance largely affected by community properties such as initial biomass, sample types and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the “PMA-responsive” microbes, we compared our results with previous PMA-based studies and found that PMA-responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. Conclusions: This study provides a comprehensive evaluation of PMA-seq exploring its quantitative accuracy in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities, but provided only qualitative assessments in realistically complex community samples.

Effect of Dapagliflozin on Intestinal Flora in MafA-deficient Mice

2018 ◽  
Vol 24 (27) ◽  
pp. 3223-3231 ◽  
Author(s):  
Luyao Li ◽  
Shiyao Xu ◽  
Tingting Guo ◽  
Shouliang Gong ◽  
Chuan Zhang
Keyword(s):  
Blood Glucose ◽  
High Throughput Sequencing ◽  
Fatty Acid Content ◽  
Fasting Blood Glucose ◽  
Intestinal Flora ◽  
Short Chain Fatty Acids ◽  
The Body ◽  
Short Chain ◽  
Control Group ◽  
Deficient Mice

Objective: To investigate the effect of dapagliflozin on intestinal microflora in MafA-deficient mice using an animal model of diabetes. Methods: Male MafA-deficient mice were administered dapagliflozin (1.0 mg/kg/d) intragastrically for 6 weeks. Mouse body weights and fasting blood glucose levels were measured, and intestinal short-chain fatty acids were measured by gas chromatography. A series of methods was used to analyse the number of primary harmful bacteria in the faeces, and high-throughput sequencing was used to sequence the changes in intestinal flora. Results: The weight of the mice decreased after dapagliflozin gavage, and fasting blood glucose was significantly lower than that in the control group (P < 0.001). Acetic acid and butyric acid contents in the intestinal tracts of the mice increased, and the growth of harmful microorganisms, such as Clostridium perfringens, enterococci, Enterobacteriaceae, and intestinal enterococci, was inhibited. Blautia is a species found in the experimental group and was significantly different from the control and blank groups as determined by the LDA score from highthroughput sequencing. Conclusion: Dapagliflozin can reduce fasting blood glucose, decrease body weight, increase short-chain fatty acid content, regulate the intestinal microecological balance of the body and promote blood glucose and energy homeostasis.

scholarly journals Extremely Halophilic Biohydrogen Producing Microbial Communities from High-Salinity Soil and Salt Evaporation Pond

Fuels ◽  
2021 ◽  
Vol 2 (2) ◽  
pp. 241-252
Author(s):  
Dyah Asri Handayani Taroepratjeka ◽  
Tsuyoshi Imai ◽  
Prapaipid Chairattanamanokorn ◽  
Alissara Reungsang
Keyword(s):  
Microbial Communities ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
High Salinity ◽  
Amplicon Sequencing ◽  
Spatial Proximity ◽  
Lignocellulosic Waste ◽  
Evaporation Pond ◽  
Operational Taxonomic Units ◽  
Determining Factor

Extreme halophiles offer the advantage to save on the costs of sterilization and water for biohydrogen production from lignocellulosic waste after the pretreatment process with their ability to withstand extreme salt concentrations. This study identifies the dominant hydrogen-producing genera and species among the acclimatized, extremely halotolerant microbial communities taken from two salt-damaged soil locations in Khon Kaen and one location from the salt evaporation pond in Samut Sakhon, Thailand. The microbial communities’ V3–V4 regions of 16srRNA were analyzed using high-throughput amplicon sequencing. A total of 345 operational taxonomic units were obtained and the high-throughput sequencing confirmed that Firmicutes was the dominant phyla of the three communities. Halanaerobium fermentans and Halanaerobacter lacunarum were the dominant hydrogen-producing species of the communities. Spatial proximity was not found to be a determining factor for similarities between these extremely halophilic microbial communities. Through the study of the microbial communities, strategies can be developed to increase biohydrogen molar yield.

scholarly journals Gluten-degrading bacteria: availability and applications

2021 ◽  
Author(s):  
Viia Kõiv ◽  
Tanel Tenson
Keyword(s):  
Microbial Communities ◽  
Digestive Tract ◽  
Storage Proteins ◽  
Gluten Free Diet ◽  
Natural Food ◽  
Gluten Free ◽  
Efficient Treatment ◽  
Gluten Intolerance ◽  
Degrading Bacteria ◽  
Human Digestive Tract

Abstract Gluten is a mixture of storage proteins in wheat and occurs in smaller amounts in other cereal grains. It provides favorable structure to bakery products but unfortunately causes disease conditions with increasing prevalence. In the human gastrointestinal tract, gluten is cleaved into proline and gluten rich peptides that are not degraded further. These peptides trigger immune responses that might lead to celiac disease, wheat allergy, and non-celiac gluten sensitivity. The main treatment option is a gluten-free diet. Alternatively, using enzymes or microorganisms with gluten-degrading properties might alleviate the disease. These components can be used during food production or could be introduced into the digestive tract as food supplements. In addition, natural food from the environment is known to enrich the microbial communities in gut and natural environmental microbial communities have high potential to degrade gluten. It remains to be investigated if food and environment-induced changes in the gut microbiome could contribute to the triggering of gluten-related diseases. Key points • Wheat proteins, gluten, are incompletely digested in human digestive tract leading to gluten intolerance. • The only efficient treatment of gluten intolerance is life-long gluten-free diet. • Environmental bacteria acquired together with food could be source of gluten-degrading bacteria detoxifying undigested gluten peptides.

Differential effects of early-life and post-weaning galactooligosaccharides intervention on colonic bacterial composition and function in weaning piglets

2021 ◽  
Author(s):  
Shiyi Tian ◽  
Jue Wang ◽  
Jing Wang ◽  
Weiyun Zhu
Keyword(s):  
Gene Expression ◽  
Early Life ◽  
Short Chain Fatty Acids ◽  
Combined Effect ◽  
Economic Losses ◽  
Swine Industry ◽  
Bacterial Composition ◽  
Colonic Microbiota ◽  
Α Diversity ◽  
Weaning Piglets

Recently, we have proved that the early-life galactooligosaccharides (GOS) intervention could improve the colonic function by altering the bacterial composition in the suckling piglets. However, whether the early-life GOS (ELG) intervention could have a long influence of the colonic microbiota, and the ELG and post-weaning GOS (PWG) combined intervention would have an interaction effect on maintaining colonic health in weaning piglets remain to be explored. Thus in this study, we illustrated the differential effect of ELG and PWG intervention on colonic microbiota and colonic function of weaning piglets. Our results showed that both the ELG and PWG intervention decreased the diarrhea frequency of weaning piglets, while the PWG intervention increased colonic indexes. After 16S rRNA MiSeq sequencing of gut bacteria belonged to colonic niches (mucosa and digesta), the PWG increased the α-diversity of colonic mucosal bacteria was revealed. In addition, we found both the ELG and PWG intervention enriched the abundance of short chain fatty acids (SCFAs) producer in different colonic niches and increased total SCFAs concentrations in colonic digesta. These changes selectively modulated the mRNA expression of pattern recognition receptors and barrier proteins in the colonic mucosa. Of note, the combined effect of ELG and PWG effectively enhanced colonic SCFAs producer enrichment and up-regulated the butyrate concentration. Meanwhile, the gene expression of MyD88-NFκB signaling and the pro-inflammatory cytokines contents were markedly reduced under the combined effect of ELG and PWG. Importance Reducing the disorders of gut ecosystem is an effective way to relieve weaning stresses of piglets and save economic losses in the modern swine industry. To this end, prebiotics were often added in diet during the weaning transition. In present study, we demonstrated that the ELG and PWG intervention had shown different effects on the bacterial composition of different colonic niches and colonic function in the weaning piglets. Especially under the combined effect of ELG and PWG intervention, the gene expression of MyD88-NFκB signaling and the contents of pro-inflammation cytokines decreased with the increasing concentration of butyrate, which is one of the important microbial metabolites in the colon of weaning piglets. These findings further provided new insights into nutritional interventions to alleviate intestinal ecosystem dysbiosis and gut dysfunction in the piglets during the weaning transition.

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