scholarly journals Taxonomic and functional dissimilarities of soil bacterial communities are more related to environmental dissimilarity than geographic distance

2021 ◽  
Author(s):  
Qingqing Liang ◽  
Heidi Mod ◽  
Shuaiwei Luo ◽  
Beibei Ma ◽  
Kena Yang ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Environmental Filtering ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Tibet Plateau ◽  
Environmental Predictors ◽  
N Dynamics ◽  
Soil Bacterial Communities ◽  
Functional Community ◽  
16S Amplicon Sequencing

The processes governing soil bacteria biogeography are still not fully understood. It remains unknown how the importance of environmental filtering and dispersal differs between bacterial taxonomic and functional biogeography, and whether their importance is scale-dependent. We sampled soils at 195 plots across the Tibet plateau, with distances among plots ranging from 20 m to 1 550 km. Taxonomic composition of bacterial community was characterized by 16S amplicon sequencing, and functional community composition by qPCR targeting 9 functional groups involved in N dynamics. Twelve climatic and soil characteristics were also measured. Both taxonomic and functional dissimilarities were more related to environmental dissimilarity than geographic distance. Taxonomic dissimilarity was mostly explained by soil pH and organic matter, while functional dissimilarity was mostly linked to moisture, temperature and N, P and C availabilities. The roles of environmental filtering and dispersal were, however, scale-dependent and varied between taxonomic and functional dissimilarities, with distance affecting taxonomic dissimilarity over short distances (<~300 km) and functional dissimilarity over long distances (>~600 km). The importance of different environmental predictors varied across scales more for functional than taxonomic dissimilarity. Our results demonstrate how biodiversity dimension (taxonomic versus functional) and spatial scale strongly influence the conclusions derived from bacterial biogeography studies.

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 Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 472
Author(s):  
Yeong-Ji Oh ◽  
Ye-Rin Park ◽  
Jungil Hong ◽  
Do-Yup Lee
Keyword(s):  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Functional Evaluation ◽  
Initial Condition ◽  
Microbial Composition ◽  
Light Emitting ◽  
Blue Led ◽  
Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

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 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.

Changes in the gut microbiota of morbidly obese patients after laparoscopic sleeve gastrectomy

2021 ◽  
Author(s):  
Alev Kural ◽  
Imran Khan ◽  
Hakan Seyit ◽  
Tuba R Caglar ◽  
Pınar Toklu ◽  
...  
Keyword(s):  
Sleeve Gastrectomy ◽  
Gut Microbiota ◽  
Laparoscopic Sleeve Gastrectomy ◽  
Amplicon Sequencing ◽  
Morbidly Obese ◽  
Microbiota Composition ◽  
16S Amplicon Sequencing ◽  
Before And After ◽  
Stool Samples ◽  
Gut Microbiota Composition

Aims: Permanent treatment of morbid obesity with medication or diet is nearly impossible. Laparoscopic sleeve gastrectomy (LSG) is becoming a widely accepted treatment option. This study profiled and compared gut microbiota composition before and after LSG. Methods & results: A total of 54 stool samples were collected from 27 morbidly obese individuals before and after LSG. The gut microbiota was profiled with 16S amplicon sequencing. After LSG, patients demonstrated a significant decrease (p < 0.001) in BMI and an increase in bacterial diversity. An increased Firmicutes/Bacteroidetes ratio was also noticed after LSG. The families Prevotellaceae and Veillonellaceae predominated in preoperative samples but were markedly lowered after LSG. A marked increase in Akkermansia, Alistipes, Streptococcus, Ruminococcus and Parabacteroides was observed after LSG. Conclusion: In addition to lowering BMI, LSG remodeled gut microbiota composition.

Temporal variation in soil bacterial communities can be confounded with spatial variation

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Syrie M Hermans ◽  
Hannah L Buckley ◽  
Fiona Curran-Cournane ◽  
Matthew Taylor ◽  
Gavin Lear
Keyword(s):  
Temporal Variation ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Spatial Distance ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Causal Processes ◽  
Fundamental Understanding ◽  
Soil Bacterial ◽  
Indigenous Forest

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P &lt; 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (&lt;1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

scholarly journals The roles of environmental variation and spatial distance in explaining diversity and biogeography of soil denitrifying communities in remote Tibetan wetlands

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
Xiaoliang Jiang ◽  
Wenzhi Liu ◽  
Lunguang Yao ◽  
Guihua Liu ◽  
Yuyi Yang
Keyword(s):  
Electrical Conductivity ◽  
Soil Moisture ◽  
Soil Temperature ◽  
Community Composition ◽  
Environmental Filtering ◽  
Operational Taxonomic Unit ◽  
Amplicon Sequencing ◽  
Spatial Distance ◽  
Wetland Type ◽  
Α Diversity

ABSTRACT The relative importance of local environments and dispersal limitation in shaping denitrifier community structure remains elusive. Here, we collected soils from 36 riverine, lacustrine and palustrine wetland sites on the remote Tibetan Plateau and characterized the soil denitrifier communities using high-throughput amplicon sequencing of the nirS and nirK genes. Results showed that the richness of nirS-type denitrifiers in riverine wetlands was significantly higher than that in lacustrine wetlands but not significantly different from that in palustrine wetlands. There was no clear distinction in nir community composition among the three kinds of wetlands. Irrespective of wetland type, the soil denitrification rate was positively related to the abundance, but not the α-diversity, of denitrifying communities. Soil moisture, carbon availability and soil temperature were the main determinants of diversity [operational taxonomic unit (OTU) number] and abundance of thenirS-type denitrifier community, while water total organic carbon, soil NO3– and soil moisture were important in controlling nirK-type denitrifier diversity and abundance. The nirS community composition was influenced by water electrical conductivity, soil temperature and water depth, while the nirK community composition was affected by soil electrical conductivity. Spatial distance explained more variation in the nirS community composition than in the nirK community composition. Our findings highlight the importance of both environmental filtering and spatial distance in explaining diversity and biogeography of soil nir communities in remote and relatively undisturbed wetlands.

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