Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake

2018 ◽  
Vol 64 (11) ◽  
pp. 786-797 ◽  
Author(s):  
Zhaoyu Kong ◽  
Wenbo Kou ◽  
Yantian Ma ◽  
Haotian Yu ◽  
Gang Ge ◽  
...  
Keyword(s):  
Water Level ◽  
Relative Abundance ◽  
Poyang Lake ◽  
Nutrient Status ◽  
Diversity Indices ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Bacterioplankton Community ◽  
Α Diversity ◽  
Composition Structure

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring–winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

Pilot trial of vitamin D3 and calcifediol in healthy vitamin D deficient adults: does it change the fecal microbiome?

2021 ◽  
Author(s):  
Albert Shieh ◽  
S Melanie Lee ◽  
Venu Lagishetty ◽  
Carter Gottleib ◽  
Jonathan P Jacobs ◽  
...  
Keyword(s):  
Vitamin D ◽  
Vitamin D Deficiency ◽  
Relative Abundance ◽  
Vitamin D3 ◽  
Pilot Trial ◽  
Fecal Microbiota ◽  
Small Sample ◽  
Rrna Gene ◽  
Β Diversity ◽  
Α Diversity

Abstract Purpose To determine whether correcting vitamin D deficiency with cholecalciferol (vitamin D3, D3) or calcifediol (25-hydroxyvitamin D3, 25(OH)D3) changes gut microbiome composition. Methods 18 adults with vitamin D deficiency (25-hydroxyvitamin D [25(OH)D] <20 ng/ml) received 60 mcg/day of D3 or 20 mcg/day of 25(OH)D3 for 8 weeks. Changes in serum 25(OH)D, 1,25-diydroxyvitamin D (1,25(OH)2D), and 24,25-dihydroxyvitamin D (24,25(OH)2D) were assessed. We characterized composition of the fecal microbiota using 16S rRNA gene sequencing, and examined changes in α-diversity (Chao 1, Faith’s Phylogenetic Diversity, Shannon Index), β-diversity (DEICODE), and genus-level abundances (DESeq2). Results Vitamin D3 and 25(OH)D3 groups were similar. After 8 weeks of vitamin D3, mean 25(OH)D and 24,25(OH)2D increased significantly, but 1,25(OH)2D did not (25(OH)D: 17.8 to 30.1 ng/ml [p=0.002]; 24,25(OH)2D: 1.1 to 2.7 ng/ml [p=0.003]; 1,25(OH)2D: 49.5 to 53.0 pg/ml [p=0.9]). After 8 weeks of 25(OH)D3, mean 25(OH)D, 24,25(OH)2D, and 1,25(OH)2D increased significantly (25(OH)D: 16.7 to 50.6 ng/ml [p<0.0001]; 24,25(OH)2D: 1.3 to 6.2 ng/ml [p=0.0001]; 1,25(OH)2D: 56.5 to 74.2 pg/ml [p=0.05]). Fecal microbial α-diversity and β-diversity did not change with D3 or 25D3 supplementation. Mean relative abundance of Firmicutes increased and mean relative abundance of Bacterioidetes decreased from baseline to four weeks, but returned to baseline by study completion. DESeq2 analysis did not confirm any statistically significant taxonomic changes. Main conclusions In a small sample of healthy adults with vitamin D deficiency, restoration of vitamin D sufficiency with vitamin D3 or 25(OH)D3 did not lead to lasting changes in the fecal microbiota.

Water-level fluctuations affect the alpha and beta diversity of macroinvertebrates in Poyang Lake, China

2020 ◽  
Author(s):  
Chaozhong Tan ◽  
Tianjin Sheng ◽  
Lizhu Wang ◽  
Evance Mbao ◽  
Jin Gao ◽  
...  
Keyword(s):  
Water Level ◽  
Beta Diversity ◽  
Poyang Lake ◽  
High Water ◽  
Freshwater Ecosystems ◽  
Water Level Fluctuations ◽  
Spatial And Temporal Variability ◽  
Alpha And Beta Diversity ◽  
Β Diversity ◽  
Α Diversity

Water-level fluctuations (WLFs) are a key influence on aquatic biodiversity in seasonally inundatedfreshwater ecosystems. However, how unregulated WLFs affect macroinvertebrates in lake-floodplain systemsexperiencing considerable annual fluctuations remains unclear. We explored spatial and temporal variability intaxonomic α and β diversity in the largest fluctuating lake in China, Poyang Lake, during two hydrological seasons.We hypothesized that taxa richness (α diversity) is greater in the floodplain than in the lake channel due to greateravailability of trophic resources, and that variability in assemblage composition (β diversity) in the channel isgreater during the high-water season (HWS) than the low-water season (LWS) due to increased habitat heterogeneity.Benthic macroinvertebrate assemblages were sampled, water physicochemical and hydrological variables weremeasured, and geographical coordinates were determined at 34 sites during the HWS (October 2017) and LWS(January and April 2018). A total of 74 taxa were recorded. Macroinvertebrate α diversity was comparable in thefloodplain and the lake channel. Beta diversity in the channel was greater during HWS than LWS. Hydrologicalvariables influenced β diversity during LWS and geographical distance between sites increased β diversity duringHWS, whereas physicochemical variables did not influence β diversity in either hydrological season. Our resultssuggest that extensive WLFs altered macroinvertebrate biodiversity among hydrological seasons by extending waterinto floodplains during HWS and reducing substrate heterogeneity in the lake channel during LWS. We thushighlight the importance of WLFs that maintain such environmental seasonality in supporting the biodiversity ofbenthic macroinvertebrates in naturally dynamic freshwater ecosystems.

scholarly journals Preventive Effects and Mechanisms of Garlic on Dyslipidemia and Gut Microbiome Dysbiosis

Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1225 ◽  
Author(s):  
Keyu Chen ◽  
Kun Xie ◽  
Zhuying Liu ◽  
Yasushi Nakasone ◽  
Kozue Sakao ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Density Lipoprotein ◽  
16S Rrna Gene Sequencing ◽  
Normal Diet ◽  
Rrna Gene ◽  
Organosulfur Compounds ◽  
Model Assessment ◽  
Α Diversity ◽  
Homeostatic Model Assessment

Garlic (Allium sativum L.) contains prebiotic components, fructans, antibacterial compounds, and organosulfur compounds. The complex ingredients of garlic seem to impart a paradoxical result on the gut microbiome. In this study, we used a mouse model to clarify the effects of whole garlic on the gut microbiome. C57BL/6N male mice were fed with or without whole garlic in normal diet (ND) or in high-fat diet (HFD) for 12 weeks. Supplementation with whole garlic attenuated HFD-enhanced ratio of serum GPT/GOT (glutamic-pyruvic transaminase/glutamic-oxaloacetic transaminase), levels of T-Cho (total cholesterol) and LDLs (low-density lipoproteins), and index of homeostatic model assessment for insulin resistance (HOMA-IR), but had no significant effect in the levels of serum HDL-c (high density lipoprotein cholesterol), TG (total triacylglycerol), and glucose. Moreover, garlic supplementation meliorated the HFD-reduced ratio of villus height/crypt depth, cecum weight, and the concentration of cecal organic acids. Finally, gut microbiota characterization by high throughput 16S rRNA gene sequencing revealed that whole garlic supplementation increased the α-diversity of the gut microbiome, especially increasing the relative abundance of f_Lachnospiraceae and reducing the relative abundance of g_Prevotella. Taken together, our data demonstrated that whole garlic supplementation could meliorate the HFD-induced dyslipidemia and disturbance of gut microbiome.

scholarly journals Ruminal and Fecal Bacteriome of Dairy Calves Fed Different Levels and Sources of NDF

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2705
Author(s):  
Gercino Ferreira Virgínio Júnior ◽  
Ana Paula da Silva ◽  
Ariany Faria de Toledo ◽  
Milaine Poczynek ◽  
Amanda Moelemberg Cezar ◽  
...  
Keyword(s):  
Basal Diet ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Ruminal Fluid ◽  
Fecal Samples ◽  
Α Diversity ◽  
Holstein Calves ◽  
Hind Gut ◽  
Different Levels

A starter concentrate containing different levels and sources of NDF can modify the gastrointestinal bacteriome. This study evaluated 18 Holstein calves housed in un-bedded suspended individual cages, fed one of three treatments: 22NDF: a conventional starter containing 22% NDF (n = 7); 31NDF: a starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22Hay: diet 22NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily, weaned at 8th week of age, and housed in wood shelters until week 10. To evaluate the bacteriome, the bacterial community of ruminal fluid and fecal samples was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene. Bacterial diversity in rumen was not affected by diet or age. The phyla Firmicutes and Bacteroidota, and Prevotella’ genus were the most abundant in ruminal fluid and fecal samples. In feces, the α-diversity indices were higher for 22Hay. All indices were significantly affected by age. We believe that the ruminal bacteriome was affected by basal diet components, but not affected by NDF levels or sources. The supply of hay was effective in modifying the fecal bacteriome of dairy calves due to hind gut fermentation.

scholarly journals Observational Cohort Study of Oral Mycobiome and InterKingdom Interactions over the Course of Induction Therapy for Leukemia

mSphere ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Sarah Robinson ◽  
Christine B. Peterson ◽  
Pranoti Sahasrabhojane ◽  
Nadim J. Ajami ◽  
Samuel A. Shelburne ◽  
...  
Keyword(s):  
Relative Abundance ◽  
High Intensity ◽  
Network Connectivity ◽  
Illumina Miseq ◽  
Study Data ◽  
Remission Induction ◽  
Rrna Gene ◽  
Α Diversity ◽  
Clinical Consequences ◽  
Observational Cohort

ABSTRACT Although the term “microbiome” refers to all microorganisms, the majority of microbiome studies focus on the bacteriome. Here, we characterize the oral mycobiome, including mycobiome-bacteriome interactions, in the setting of remission-induction chemotherapy (RIC) for acute myeloid leukemia (AML). Oral samples (n = 299) were prospectively collected twice weekly from 39 AML patients during RIC until neutrophil recovery. Illumina MiSeq 16S rRNA gene (V4) and internal transcribed spacer 2 (ITS2) sequencing were used to determine bacterial and fungal diversity and community composition. Intrakingdom and interkingdom network connectivity at baseline (T1) and at midpoint (T3) and a later time point (T6) were assessed via SPIEC-EASI (sparse inverse covariance estimation for ecological association inference). In this exploratory study, mycobiome α-diversity was not significantly associated with antibiotic or antifungal receipt. However, postchemotherapy mycobiome α-diversity was lower in subjects receiving high-intensity chemotherapy. Additionally, greater decreases in Malassezia levels were seen over time among patients on high-intensity RIC compared to low-intensity RIC (P = 0.003). A significantly higher relative abundance of Candida was found among patients who had infection (P = 0.008), while a significantly higher relative abundance of Fusarium was found among patients who did not get an infection (P = 0.03). Analyses of intrakingdom and interkingdom relationships at T1, T3, and T6 indicated that interkingdom connectivity increased over the course of IC as bacterial α-diversity diminished. In (to our knowledge) the first longitudinal mycobiome study performed during AML RIC, we found that mycobiome-bacteriome interactions are highly dynamic. Our study data suggest that inclusion of mycobiome analysis in the design of microbiome studies may be necessary to optimally understand the ecological and functional role of microbial communities in clinical outcomes. IMPORTANCE This report highlights the importance of longitudinal, parallel characterization of oral fungi and bacteria in order to better elucidate the dynamic changes in microbial community structure and interkingdom functional interactions during the injury of chemotherapy and antibiotic exposure as well as the clinical consequences of these interrelated alterations.

scholarly journals Significant changes in the bacterioplankton community structure of a maritime Antarctic freshwater lake following nutrient enrichment

Microbiology ◽  
2005 ◽  
Vol 151 (10) ◽  
pp. 3237-3248 ◽  
Author(s):  
David A. Pearce ◽  
Christopher J. van der Gast ◽  
Kelly Woodward ◽  
Kevin K. Newsham
Keyword(s):  
Population Density ◽  
Environmental Change ◽  
Nutrient Enrichment ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Acid Methyl Ester ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Maritime Antarctic ◽  
Lake Chemistry ◽  
Bacterioplankton Community

Nutrient enrichment is known to increase bacterioplankton population density in a variety of Antarctic freshwater lakes. However, relatively little is known about the associated changes in species composition. In this study, the bacterioplankton community composition of one such lake was studied following natural nutrient enrichment to investigate the resistance of the system to environmental change. Heywood Lake is an enriched freshwater maritime Antarctic lake, with nitrogen and phosphorus concentrations significantly higher than its more oligotrophic neighbours (by at least an order of magnitude). This major change in lake chemistry has occurred following large increases in the fur seal population over the last 30 years. Using analysis of 16S rRNA gene fragments, fatty acid methyl ester analysis, denaturing gradient gel electrophoresis and fluorescence in situ hybridization, significant changes are reported in lake microbiology which have resulted in a distinct bacterioplankton community. In comparison to its more oligotrophic neighbours, nutrient-enriched Heywood Lake has a high bacterioplankton population density, reduced species richness and an increasing evenness among key groups. Only 42·3 % of the clones found with ≥97 % similarity to a named genus were also present in adjacent oligotrophic lakes, including three of the dominant groups. Critically, there was an apparent shift in dominance with trophic status (from the β-Proteobacteria to the Actinobacteria). Other key observations included the absence of a dominant group of Cyanobacteria and the presence of marine bacteria. The significant impact of natural nutrient enrichment on the microbiology of Heywood Lake, therefore, suggests that low-temperature oligotrophic freshwater lake systems might have low resistance to environmental change.

scholarly journals Comparison of the human microbiome in adults and children with chronic rhinosinusitis

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0242770
Author(s):  
Il-Ho Park ◽  
Joong Seob Lee ◽  
Joo-Hoo Park ◽  
Sung Hun Kang ◽  
Seok Min Hong ◽  
...  
Keyword(s):  
Chronic Rhinosinusitis ◽  
Relative Abundance ◽  
Treatment Options ◽  
Human Microbiome ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Group Method ◽  
Rrna Gene ◽  
Adult Group ◽  
Adults And Children

We hypothesized that differences in the microbiome could be a cause of the substantial differences in the symptoms of and treatment options for adult and pediatric patients with chronic rhinosinusitis (CRS). First, we characterized the differences in the nasal microbiomes of pediatric and adult CRS patients. Swabs were obtained from 19 patients with chronic rhinosinusitis (9 children and 10 adults). The bacterial 16S rRNA gene was pyrosequenced to compare the microbiota of the middle meatus. No significant differences were found in species richness and alpha-diversity indices between the two groups. However, in the comparison of diversity between groups using the unweighted pair group method with arithmetic mean (UPGMA) clustering of microbiome taxonomic profiles, we observed a relatively clear separation between the adult and pediatric groups. Actinobacteria had a significantly higher relative abundance in the adult group than in the pediatric group at the phylum level. At the genus level, Corynebacterium showed significantly higher relative abundance in the adult group than in the pediatric group. This is a comparative study between the microbiomes of adult and pediatric CRS patients. We expect this study to be the first step in understanding the pathogenesis of CRS in adults and children using microbiome analysis.

scholarly journals Diversity of bird communities of the forest in the Boyarska experimental station at the gradient of anthropic load

2020 ◽  
Vol 11 (3) ◽  
Author(s):  
V.A. Gaychenko ◽  
◽  
T.V. Shupova ◽  
Keyword(s):  
Species Composition ◽  
Relative Abundance ◽  
Conservation Status ◽  
Bird Species ◽  
Parus Major ◽  
Diversity Indices ◽  
Bird Communities ◽  
Experimental Station ◽  
Α Diversity ◽  
Synanthropization Index

Bird communities was researched according to the transect method in the nesting period of 2013 and 2015. 4 model forest plots in the Boyarskaya Experimental Station were selected. All of them are culturelphytocenoses based onPinus sylvestris L., Quercus robur L., Q. rubra L. The species composition of birds, their abundance, α-diversity indices, synanthropization index of bird communities (to Jedryctkowski) were analyzed. The similarity of bird communities was determined using cluster analysis in "Origin Pro 9.0". 65 bird species of 11 orders were recorded. 35 species of them live in the species reserve. On model plots that not have conservation status, the number of species in bird communities is 20–27. In plots with a dominance of Q. robur, 42 species were recorded, with a dominance of P. sylvestris - 35 species of the birds. Dominants in bird communities Parus major L. and Fringilla coelebs L. The presence in the list of subdominants Anthus trivialis L. and Phylloscopus sibilatrix Bechstein is a positive characteristic of the forest. The synanthropic of bird communities increases according to the increase in anthropic load: the synanthropization index from 0.4 to 0.65, the relative abundance of synanthropic birds in communities from 0.66 to 0.81. There are no alien birds. The species diversity and the number of bird species in the communities decreases along the gradient of increasing anthropic load. The similarity of bird communities and their α-diversity depends by the anthropic load, and not by the ratio of the species composition of the forest trees. The distribution of relative abundance of species in bird communities, on the contrary, is associated with the ratio of the species composition of trees. In forest plots dominated by P. sylvestris, bird communities are balanced, in plots with a predominance of Q. robur, disturbances in the development of bird communities are noticeable.

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