1621 Comparisons of microbial populations found in the rumen and in a dual-flow continuous culture fermentation system using high-throughput 16S amplicon sequencing

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 789-789
Author(s):  
I. J. Salfer ◽  
H. E. Larson ◽  
M. D. Stern
Keyword(s):  
Continuous Culture ◽  
High Throughput ◽  
Amplicon Sequencing ◽  
Microbial Populations ◽  
Fermentation System ◽  
16S Amplicon Sequencing

scholarly journals Laboratory growth of denitrifying water column microbial consortia from deep-sea shipwrecks in the northern Gulf of Mexico

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1834
Author(s):  
Dhanya Haridas ◽  
Justin C. Biffinger ◽  
Thomas J. Boyd ◽  
Preston A. Fulmer ◽  
Leila J. Hamdan ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Water Column ◽  
Deep Sea ◽  
Amplicon Sequencing ◽  
Microbial Consortia ◽  
Microbial Populations ◽  
Northern Gulf Of Mexico ◽  
Metabolic Adaptations ◽  
16S Amplicon Sequencing ◽  
Growth Profiles

Background: Shipwrecks serve as a rich source for novel microbial populations that have largely remained undiscovered. Low temperatures, lack of sunlight, and the availability of substrates derived from the shipwreck’s hull and cargo may provide an environment in which microbes can develop unique metabolic adaptations.  Methods: To test our hypothesis that shipwrecks could influence the microbial population involved in denitrification when a consortium is grown in the laboratory, we collected samples proximate to two steel shipwrecks in the northern Gulf of Mexico. Then under laboratory conditions, we grew two independent denitrifying microbial consortia. Each consortium was grown by using the BART assay system and analyzed based on growth kinetics, ion chromatography and 16S amplicon sequencing.Results: Both denitrifying consortia were different from each other based on varied growth profiles, rates of nitrate utilization and 16S amplicon sequencing.Conclusions: Our observations conclude that the laboratory grown water column microbial consortia from deep-sea shipwrecks in the Gulf of Mexico are able to undergo aggressive denitrification.

scholarly journals Laboratory growth of denitrifying water column microbial consortia from deep-sea shipwrecks in the northern Gulf of Mexico

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1834 ◽  
Author(s):  
Dhanya Haridas ◽  
Justin C. Biffinger ◽  
Thomas J. Boyd ◽  
Preston A. Fulmer ◽  
Leila J. Hamdan ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Water Column ◽  
Deep Sea ◽  
Amplicon Sequencing ◽  
Microbial Consortia ◽  
Microbial Populations ◽  
Northern Gulf Of Mexico ◽  
Metabolic Adaptations ◽  
16S Amplicon Sequencing ◽  
Growth Profiles

Background: Shipwrecks serve as a rich source for novel microbial populations that have largely remained undiscovered. Low temperatures, lack of sunlight, and the availability of substrates derived from the shipwreck’s hull and cargo may provide an environment in which microbes can develop unique metabolic adaptations.  Methods: To test our hypothesis that shipwrecks could influence the microbial population involved in denitrification when a consortium is grown in the laboratory, we collected samples proximate to two steel shipwrecks in the northern Gulf of Mexico. Then under laboratory conditions, we grew two independent denitrifying microbial consortia. Each consortium was grown by using the BART assay system and analyzed based on growth kinetics, ion chromatography and 16S amplicon sequencing.Results: Both denitrifying consortia were different from each other based on varied growth profiles, rates of nitrate utilization and 16S amplicon sequencing.Conclusions: Our observations conclude that the laboratory grown water column microbial consortia from deep-sea shipwrecks in the Gulf of Mexico are able to undergo aggressive denitrification.

scholarly journals Laboratory growth of denitrifying water column microbial consortia from deep-sea shipwrecks in the northern Gulf of Mexico

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 1834 ◽  
Author(s):  
Dhanya Haridas ◽  
Justin C. Biffinger ◽  
Thomas J. Boyd ◽  
Preston A. Fulmer ◽  
Leila J. Hamdan ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Water Column ◽  
Deep Sea ◽  
Amplicon Sequencing ◽  
Microbial Consortia ◽  
Microbial Populations ◽  
Northern Gulf Of Mexico ◽  
Metabolic Adaptations ◽  
16S Amplicon Sequencing ◽  
Growth Profiles

Background: Shipwrecks serve as a rich source for novel microbial populations that have largely remained undiscovered. Low temperatures, lack of sunlight, and the availability of substrates derived from the shipwreck’s hull and cargo may provide an environment in which microbes can develop unique metabolic adaptations.  Methods: To test our hypothesis that shipwrecks could influence the microbial population involved in denitrification when a consortium is grown in the laboratory, we collected samples proximate to two steel shipwrecks in the northern Gulf of Mexico. Then under laboratory conditions, we grew two independent denitrifying microbial consortia. Each consortium was grown by using the BART assay system and analyzed based on growth kinetics, ion chromatography and 16S amplicon sequencing.Results: Both denitrifying consortia were different from each other based on varied growth profiles, rates of nitrate utilization and 16S amplicon sequencing.Conclusions: Our observations conclude that the laboratory grown water column microbial consortia from deep-sea shipwrecks in the Gulf of Mexico are able to undergo aggressive denitrification.

scholarly journals SARS-CoV-2 does not have a strong effect on the nasopharyngeal microbial composition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tzipi Braun ◽  
Shiraz Halevi ◽  
Rotem Hadar ◽  
Gilate Efroni ◽  
Efrat Glick Saar ◽  
...  
Keyword(s):  
Clinical Microbiology ◽  
Amplicon Sequencing ◽  
Viral Disease ◽  
Nasopharyngeal Swab ◽  
Microbial Composition ◽  
16S Amplicon Sequencing ◽  
The World ◽  
Health And Disease ◽  
Longitudinal Sampling ◽  
Potential Interactions

AbstractThe coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.

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 Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Wenzhi Cui ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Large Scale ◽  
Low Cost ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
Training Sample ◽  
Rrna Gene ◽  
16S Amplicon Sequencing ◽  
Cross Platform ◽  
Functional Profiles

Abstract Background Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results. Results Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS. Conclusions This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals Larval Diet Abundance Influences Size and Composition of the Midgut Microbiota of Aedes aegypti Mosquitoes

2021 ◽  
Vol 12 ◽  
Author(s):  
Hannah J. MacLeod ◽  
George Dimopoulos ◽  
Sarah M. Short
Keyword(s):  
Aedes Aegypti ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Larval Diet ◽  
Microbiota Composition ◽  
Vector Species ◽  
Larval Food ◽  
Disease Vector ◽  
16S Amplicon Sequencing ◽  
The Impact

The midgut microbiota of the yellow fever mosquito Aedes aegypti impacts pathogen susceptibility and transmission by this important vector species. However, factors influencing the composition and size of the microbiome in mosquitoes are poorly understood. We investigated the impact of larval diet abundance during development on the composition and size of the larval and adult microbiota by rearing Aedes aegypti under four larval food regimens, ranging from nutrient deprivation to nutrient excess. We assessed the persistent impacts of larval diet availability on the microbiota of the larval breeding water, larval mosquitoes, and adult mosquitoes under sugar and blood fed conditions using qPCR and high-throughput 16S amplicon sequencing to determine bacterial load and microbiota composition. Bacterial loads in breeding water increased with increasing larval diet. Larvae reared with the lowest diet abundance had significantly fewer bacteria than larvae from two higher diet treatments, but not from the highest diet abundance. Adults from the lowest diet abundance treatment had significantly fewer bacteria in their midguts compared to all higher diet abundance treatments. Larval diet amount also had a significant impact on microbiota composition, primarily within larval breeding water and larvae. Increasing diet correlated with increased relative levels of Enterobacteriaceae and Flavobacteriaceae and decreased relative levels of Sphingomonadaceae. Multiple individual OTUs were significantly impacted by diet including one mapping to the genus Cedecea, which increased with higher diet amounts. This was consistent across all sample types, including sugar fed and blood fed adults. Taken together, these data suggest that availability of diet during development can cause lasting shifts in the size and composition of the microbiota in the disease vector Aedes aegypti.

scholarly journals Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241529
Author(s):  
Anita Silver ◽  
Sean Perez ◽  
Melanie Gee ◽  
Bethany Xu ◽  
Shreeya Garg ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ground Beetle ◽  
Amplicon Sequencing ◽  
Carabid Beetles ◽  
Secretory Cells ◽  
Pygidial Gland ◽  
Defensive Compounds ◽  
Highly Active ◽  
16S Amplicon Sequencing ◽  
Host Diet

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types—guts, and pygidial gland secretory cells (which produce defensive compounds)—were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.

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