α diversity
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2022 ◽  
Vol 12 ◽  
Author(s):  
Pei Wang ◽  
Jianping Dai ◽  
Luyun Luo ◽  
Yong Liu ◽  
Decai Jin ◽  
...  

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.


2022 ◽  
Vol 8 ◽  
Author(s):  
Lang Zhang ◽  
Yongxing Hong ◽  
Yuying Liao ◽  
Kui Tian ◽  
Haodong Sun ◽  
...  

This study aimed to evaluate the effects of dietary Lasia spinosa Thw. (LST) powder supplementation on growth performance, blood metabolites, antioxidant status, intestinal morphology, and cecal microbiome in broiler chickens. A total of 400 1-day-old male Guangxi partridge broilers (initial body weight: 42.52 ± 0.06 g) were randomly allotted to 4 dietary treatments: LST0 group (a basal diet), LST1 group (a basal diet with 1% LST powder), LST2 group (a basal diet with 2% LST powder), LST4 group (a basal diet with 4% LST powder), 10 replicates for each treatment, and 10 broilers in each treatment group. Results indicated that the average daily feed intake of broilers during 22–42 days and the average daily gain of chickens during 1–42 days significantly increased by dietary supplementation of LST powder (p < 0.01), while the feed conversion ratio during the overall periods was decreased by dietary supplementation of LST powder (p < 0.01). Except for the levels of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) in liver (p > 0.05), the levels of SOD, catalase (CAT) and GSH-Px in serum, liver, and breast muscle were significantly increased in the LST supplemented groups (p < 0.05), while the levels of reactive oxygen species (ROS) and malondialdehyde (MDA) in serum, liver, and breast muscle were significantly decreased in the LST supplemented groups (p < 0.05). Furthermore, the levels of triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C) were significantly decreased by the addition of dietary LST powder (p < 0.01), while the levels of HDL-C, Ca, Fe, Mg, and P were linearly increased by the addition of dietary LST powder (p < 0.01). With respect to the gut morphometric, crypt depth was significantly decreased by LST supplementation (p < 0.05), while villus height and the ratio of villus height to crypt depth were notably increased by LST supplementation (p < 0.05). Sequencing of 16S ribosomal RNA (16S rRNA) from the cecal contents of broilers revealed that the composition of the chicken gut microbiota was altered by LST supplementation. The α-diversity of microbiota in broilers was increased (p < 0.05) in the LST1 group, but was decreased (p < 0.05) in the LST2 and LST4 groups compared with the LST0 group. The differential genera enriched in the LST1 group, such as Bacillus, Odoribacter, Sutterella, Anaerofilum, Peptococcus, were closely related to the increased growth performance, antioxidant status, intestinal morphology, Ca, Mg, and reduced blood lipid in the treated broilers.


2022 ◽  
Vol 9 ◽  
Author(s):  
Yinghan Zhao ◽  
Tian Li ◽  
Pengshuai Shao ◽  
Jingkuan Sun ◽  
Wenjing Xu ◽  
...  

Soil microorganisms play the important role in driving biogeochemical cycles. However, it is still unclear on soil microbial community characteristics and microbial driving mechanism in rhizosphere and bulk soils of different halophyte species. In this study, we analyzed bacterial communities in the rhizosphere and bulk soils of three typical halophytes in the Yellow River Delta, i.e., Phragmites communis, Suaeda salsa, and Aeluropus sinensis, by high-throughput sequencing. The contents of total carbon, total nitrogen, and available phosphorus in rhizosphere soils of the three halophytes were significantly higher than those in bulk soils, which suggested a nutrient enrichment effect of the rhizosphere. Rhizosphere soil bacterial α-diversity of P. communis was higher than that in bulk soil, whereas bacterial α-diversity in rhizosphere soil of S. salsa and A. sinensis was lower than those in bulk soil. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes, which accounted for 31, 20.5, 16.3, and 10.3%, respectively. LDA effect size (LEfSe) analysis showed that the bacterial species with significant differences in expression abundance was obviously different in the rhizosphere and bulk soil of three halophytes. The principal component analysis (PCoA) showed that bacterial community composition was greatly different between rhizosphere and bulk soils of P. communis and S. salsa, while no difference in A. sinensis. Changed bacterial community composition was mainly ascribed to salinity in rhizosphere and bulk soils. Additionally, salinity was positively correlated with Bacteroidetes and negatively correlated with Actinobacteria and Acidobacteria. Our study clarified the variation in bacterial community structure between rhizosphere and bulk soils with soil physicochemical properties, which proved a biological reference to indicate the characteristics of saline and alkaline land.


2022 ◽  
Vol 8 ◽  
Author(s):  
Ruolin Li ◽  
Yu Guo ◽  
Chuanxin Qin ◽  
Shuo Zhang ◽  
Dongping Ji ◽  
...  

Artificial habitat deployment can restore natural habitats or supplement existing natural habitats. The effect of resource proliferation and protection is obvious. However, few reports have addressed the biological community association between artificial habitats and adjacent environments. Here, Illumina sequencing of 18S rDNA was performed, and the diversity, community structure, and co-occurrence networks of protists in different layers of artificial reefs (ARs) and adjacent seawater (WAR) were described to verify that constructing ARs in Bailong Pearl Bay improves local spatial heterogeneity and functional diversity. In terms of the degree of species interaction, the protist communities were ranked as follows: surface and bottom of WAR > ARs and WAR > different layers of ARs. The α-diversity of protists associated with ARs and WAR decreased with an increase in depth. Protist diversity was greater in WAR than in ARs. β-Diversity analysis revealed significant differences in protist community structure between WAR and ARs (P < 0.05), and the upper layers of ARs and the middle or bottom layers of ARs differed. The key topological features of protist networks showed more positive interspecific interactions in the AR-associated protist community, a higher degree of niche differentiation, and higher complexity and stability. The keystone protists in the bottom seawater layer displayed community functions that were biased toward initial fixation in the ocean carbon cycle. The AR-associated protist community tended to participate in carbon transfer in the food chain and decomposition and utilization of dissolved organic matter (DOM). This study revealed significant differences in protist community structure between ARs and the adjacent environment, and the ecological functions of the key phyla were found to be related. In conclusion, protist communities in WAR may provide food sources for AR-associated heterotrophic protists. A variety of key phyla associated with ARs have biological roles in the carbon pump via their ecological characteristics.


2022 ◽  
Author(s):  
Juanita C. Rodríguez-Rodríguez ◽  
Yves Bergeron ◽  
Steven W. Kembel ◽  
Nicole J. Fenton

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.


Nutrients ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 268
Author(s):  
Joy V. Nolte Fong ◽  
Derek Miketinas ◽  
Linda W. Moore ◽  
Duc T. Nguyen ◽  
Edward A. Graviss ◽  
...  

Individual glycemic responses following dietary intake result from complex physiological processes, and can be influenced by physical properties of foods, such as increased resistant starch (RS) from starch retrogradation. Predictive equations are needed to provide personalized dietary recommendations to reduce chronic disease development. Therefore, a precision nutrition model predicting the postprandial glucose response (PPGR) in overweight women following the consumption of potatoes was formulated. Thirty overweight women participated in this randomized crossover trial. Participants consumed 250 g of hot (9.2 g RS) or cold (13.7 g RS) potatoes on two separate occasions. Baseline characteristics included demographics, 10-day dietary records, body composition, and the relative abundance (RA) and α-diversity of gut microbiota. Elastic net regression using 5-fold cross-validation predicted PPGR after potato intake. Most participants (70%) had a favorable PPGR to the cold potato. The model explained 32.2% of the variance in PPGR with the equation: 547.65 × (0 [if cold, high-RS potato], ×1, if hot, low-RS potato]) + (BMI [kg/m2] × 40.66)—(insoluble fiber [g] × 49.35) + (Bacteroides [RA] × 8.69)—(Faecalibacterium [RA] × 73.49)—(Parabacteroides [RA] × 42.08) + (α-diversity × 110.87) + 292.52. This model improves the understanding of baseline characteristics that explain interpersonal variation in PPGR following potato intake and offers a tool to optimize dietary recommendations for a commonly consumed food.


2022 ◽  
Vol 12 ◽  
Author(s):  
Guangying Cui ◽  
Shanshuo Liu ◽  
Zhenguo Liu ◽  
Yuan Chen ◽  
Tianwen Wu ◽  
...  

Objective: The gut microecosystem is the largest microecosystem in the human body and has been proven to be linked to neurological diseases. The main objective of this study was to characterize the fecal microbiome, investigate the differences between epilepsy patients and healthy controls, and evaluate the potential efficacy of the fecal microbiome as a diagnostic tool for epilepsy.Design: We collected 74 fecal samples from epilepsy patients (Eps, n = 24) and healthy controls (HCs, n = 50) in the First Affiliated Hospital of Zhengzhou University and subjected the samples to 16S rRNA MiSeq sequencing and analysis. We set up a train set and a test set, identified the optimal microbial markers for epilepsy after characterizing the gut microbiome in the former and built a diagnostic model, then validated it in the validation group.Results: There were significant differences in microbial communities between the two groups. The α-diversity of the HCs was higher than that of the epilepsy group, but the Venn diagram showed that there were more unique operational taxonomic unit (OTU) in the epilepsy group. At the phylum level, Proteobacteria and Actinobacteriota increased significantly in Eps, while the relative abundance of Bacteroidota increased in HCs. Compared with HCs, Eps were enriched in 23 genera, including Faecalibacterium, Escherichia-Shigella, Subdoligranulum and Enterobacteriaceae-unclassified. In contrast, 59 genera including Bacteroides, Megamonas, Prevotella, Lachnospiraceae-unclassified and Blautia increased in the HCs. In Spearman correlation analysis, age, WBC, RBC, PLT, ALB, CREA, TBIL, Hb and Urea were positively correlated with most of the different OTUs. Seizure-type, course and frequency are negatively correlated with most of the different OTUs. In addition, twenty-two optimal microbial markers were identified by a fivefold cross-validation of the random forest model. In the established train set and test set, the area under the curve was 0.9771 and 0.993, respectively.Conclusion: Our study was the first to characterize the gut microbiome of Eps and HCs in central China and demonstrate the potential efficacy of microbial markers as a noninvasive biological diagnostic tool for epilepsy.


Antioxidants ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 111
Author(s):  
Ying Gao ◽  
Yongquan Xu ◽  
Junfeng Yin

The prevalence of age-related cognitive impairment is increasing as the proportion of older individuals in the population grows. It is therefore necessary and urgent to find agents to prevent or ameliorate age-related cognitive impairment. Selenomethionine (SeMet) is a natural amino acid occurring in yeast and Brazil nuts. It mitigates cognitive impairment in an Alzheimer’s disease mouse model, however, whether it works on age-related cognitive impairment remains unknown. In this study, SeMet significantly improved the performance of D-galactose-treated mice in the novel object recognition test, passive avoidance task and Morris water maze test. SeMet reversed D-galactose-induced reduction of hippocampal acetylcholine levels, suppression of choline acetyltransferase activity and activation of acetyl cholinesterase. It decreased D-galactose-induced oxidative stress and increased the selenoprotein P levels in the hippocampus. Besides, it attenuated D-galactose-induced dysbiosis by increasing the α-diversity and modulating the taxonomic structure. Correlations between certain taxa and physiological parameters were observed. Our results provide evidence of the effectiveness of SeMet on ameliorating D-galactose-induced cognitive impairment and suggest SeMet has potential to be used in the prevention or adjuvant treatment of age-related cognitive impairment.


2022 ◽  
Vol 10 (1) ◽  
pp. 49
Author(s):  
Kuo-Chin Huang ◽  
Jai-Wei Lee ◽  
Ya-Li Shiu ◽  
Rolissa Ballantyne ◽  
Chun-Hung Liu

An experiment was conducted to evaluate the effects of the Micro-Aid Liquid 10 (MAL10) (DPI Global, Porterville, CA, USA), a product made from yucca extract, on growth performance, gut microbiota, and resistance of white shrimp, Litopenaeus vannamei against infectious disease caused by Vibrio alginolyticus. MAL10 was added to shrimp rearing water at different levels of 0 (control), 0.25 mL m3−1 (W0.25), 0.5 mL m3−1 (W0.5), 1 mL m3−1 (W1), and 5 mL m3−1 (W5), respectively, once per week for 70 days. Growth performances, including final body weight, specific growth rate, average daily growth and percentage of weight gain, were significantly improved by adding the MAL10 at levels up to 5 mL m3−1, which may be due to the proliferation of B cells in hepatopancreas of MAL10-treated shrimp. No significant differences in the total viable count and Vibrio-like count in the gut of shrimp were recorded by spread plate method. In the challenge test, shrimp reared in the water supplemented with MAL10 at levels of 1–5 mL m3−1 had significantly lower cumulative mortality after a challenge test with V. alginolyticus compared to shrimp reared in the control, W0.25 and W0.5 groups. Next-generation sequencing indicated that the relative distribution of phylum Proteobacteria in control (80.4%) was higher than the W (77.4%). The proportion of Vibrio was primarily dominant genera in the shrimp intestine and highest in the control group compared to the W group, followed by Spongiimonas, Motilimonas, Demequina, and Shewanella genera. Although there was no statistically significant difference, higher α-diversity indices were recorded in the W5-treated group than in the control group. Therefore, it is considered that MAL10 could be used as a natural alternative in shrimp aquaculture to reduce the risk of infectious disease caused by pathogenic Vibrio and improve the growth performance of white shrimp.


Author(s):  
Lei Huang ◽  
Haipeng Guo ◽  
Zidan Liu ◽  
Chen Chen ◽  
Kai Wang ◽  
...  

AbstractSupplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.


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