scholarly journals The hierarchy of root branching order determines bacterial composition, microbial carrying capacity and microbial filtering

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
William L. King ◽  
Caylon F. Yates ◽  
Jing Guo ◽  
Suzanne M. Fleishman ◽  
Ryan V. Trexler ◽  
...  
Keyword(s):  
Carrying Capacity ◽  
Lower Order ◽  
Tree Species ◽  
Fine Roots ◽  
Common Garden ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Branching Order ◽  
Root Branching

AbstractFine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots. To test this, we sampled roots of six temperate tree species from a 23-year-old common garden planting, separating by branching order. Rhizoplane bacterial composition was characterized with 16S rRNA gene sequencing, while bacterial abundance was determined on a subset of trees through flow cytometry. Root order strongly impacted composition across tree species, with absorptive lower order roots exerting the greatest selective pressure. Microbial carrying capacity was higher in absorptive roots in two of three tested tree species. This study indicates lower order roots as the main point of microbial interaction with fine roots, suggesting that root homogenization could mask microbial recruitment signatures.

scholarly journals Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Petra Videnska ◽  
Kristyna Smerkova ◽  
Barbora Zwinsova ◽  
Vlad Popovici ◽  
Lenka Micenkova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Isolation ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Gram Positive ◽  
Bacterial Composition ◽  
Rrna Gene Sequencing

Abstract Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.

scholarly journals Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Shinya Kageyama ◽  
Mikari Asakawa ◽  
Toru Takeshita ◽  
Yukari Ihara ◽  
Shunsuke Kanno ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Diversity ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Bacterial Composition ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

scholarly journals Dynamic Variations in Fecal Bacterial Community and Fermentation Profile of Holstein Steers in Response to Three Stepwise Density Diets

Animals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 560 ◽  
Author(s):  
Qinghua Qiu ◽  
Yangxiang Zhu ◽  
Xinjun Qiu ◽  
Chaoyu Gao ◽  
Jingjing Wang ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
High Energy ◽  
Protein Diet ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Dynamic Variations ◽  
Fermentation Profile ◽  
Relative Abundances ◽  
Protein Density ◽  
Dietary Treatments

The objective of this study was to track the dynamic variations in fecal bacterial composition and fermentation profile of finishing steers in response to three stepwise diets varied in energy and protein density. A total of 18 Holstein steers were divided into three groups in such a way that each group contained six animals and received one of three stepwise dietary treatments. Dietary treatments were C = standard energy and protein diet, H = high energy and protein diet, and L = low energy and protein diet. Animals were fattened for 11 months with a three-phase fattening strategy. Fecal samples were collected to evaluate the dynamics of fecal fermentation and bacterial composition in response to dietary treatments and fattening phases using 16S rRNA gene sequencing. Fecal acetate, propionate, and butyrate increased with increasing density of diet and as the fattening phase continued. The relative abundances of Firmicutes and Bacteroidetes dominated and showed 56.19% and 33.58%, respectively. Higher dietary density decreased the fecal bacterial diversity, Firmicutes to Bacteroidetes ratio, and the relative abundances of Ruminococcaceae_UCG-005, Rikenellaceae_RC9_gut_group, and Bacteroides, whereas higher dietary density increased the abundance of Prevotella_9. Our results indicated that both fecal fermentation profile and bacterial composition share a time-dependent variation in response to different dietary densities. This knowledge highlights that both diet and fattening phase impact fecal fermentation profile and bacterial composition, and may provide insight into strategies to reduce fecal contamination from the origin by optimizing diet and fattening time.

scholarly journals Effect of Tree Species and Mycorrhizal Colonization on the Archaeal Population of Boreal Forest Rhizospheres

2008 ◽  
Vol 75 (2) ◽  
pp. 308-315 ◽  
Author(s):  
Malin Bomberg ◽  
Sari Timonen
Keyword(s):  
16S Rrna ◽  
Boreal Forest ◽  
Tree Species ◽  
Fine Roots ◽  
Ectomycorrhizal Fungus ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Forest Trees ◽  
Detection Frequency

ABSTRACT Group 1.1c Crenarchaeota are the predominating archaeal group in acidic boreal forest soils. In this study, we show that the detection frequency of 1.1c crenarchaeotal 16S rRNA genes in the rhizospheres of the boreal forest trees increased following colonization by the ectomycorrhizal fungus Paxillus involutus. This effect was very clear in the fine roots of Pinus sylvestris, Picea abies, and Betula pendula, the most common forest trees in Finland. The nonmycorrhizal fine roots had a clearly different composition of archaeal 16S rRNA genes in comparison to the mycorrhizal fine roots. In the phylogenetic analysis, the 1.1c crenarchaeotal 16S rRNA gene sequences obtained from the fine roots formed a well-defined cluster separate from the mycorrhizal ones. Alnus glutinosa differed from the other trees by having high diversity and detection levels of Crenarchaeota both on fine roots and on mycorrhizas as well as by harboring a distinct archaeal flora. The similarity of the archaeal populations in rhizospheres of the different tree species was increased upon colonization by the ectomycorrhizal fungus. A minority of the sequences obtained from the mycorrhizas belonged to Euryarchaeota (order Halobacteriales).

scholarly journals Alterations of the Gut Microbiome and Metabolome in Patients With Proliferative Diabetic Retinopathy

2021 ◽  
Vol 12 ◽  
Author(s):  
Panpan Ye ◽  
Xueyou Zhang ◽  
Yufeng Xu ◽  
Jia Xu ◽  
Xiaoxiao Song ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Gut Microbiota ◽  
Proliferative Diabetic Retinopathy ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Diabetic Patients ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Rrna Gene Sequencing

Diabetic retinopathy (DR) has been reported to associate with gut microbiota alterations in murine models and thus “gut-retina-axis” has been proposed. However, the role of gut microbiome and the associated metabolism in DR patients still need to be elucidated. In this study, we collected fecal samples from 45 patients with proliferative diabetic retinopathy (PDR) and 90 matched diabetic patients (1:2 according to age, sex, and duration of diabetes) without DR (NDR) and performed 16S rRNA gene sequencing and untargeted metabolomics. We observed significantly lower bacterial diversity in the PDR group than that in the NDR group. Differential gut bacterial composition was also found, with significant depletion of 22 families (e.g., Coriobacteriaceae, Veillonellaceae, and Streptococcaceae) and enrichment of two families (Burkholderiaceae and Burkholderiales_unclassified) in the PDR group as compared with the NDR group. There were significantly different fecal metabolic features, which were enriched in metabolic pathways such as arachidonic acid and microbial metabolism, between the two groups. Among 36 coabundance metabolite clusters, 11 were positively/negatively contributed to PDR using logistic regression analysis. Fifteen gut microbial families were significantly correlated with the 11 metabolite clusters. Furthermore, a fecal metabolite-based classifier was constructed to distinguish PDR patients from NDR patients accurately. In conclusion, PDR is associated with reduced diversity and altered composition of gut microbiota and specific microbe-metabolite interplay. Our findings help to better understand the disease pathogenesis and provide novel diagnostic and therapeutic targets for PDR.

scholarly journals Amazonia Seasons Have an Influence in the Composition of Bacterial Gut Microbiota of Mangrove Oysters (Crassostrea gasar)

2021 ◽  
Vol 11 ◽  
Author(s):  
Marcos Vinícius Reis Conceição ◽  
Sávio Souza Costa ◽  
Ana Paula Schaan ◽  
Ândrea Kely Campos Ribeiro-dos-Santos ◽  
Artur Silva ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sampling Effort ◽  
Bacterial Composition ◽  
Bacterial Phyla ◽  
Close Relationship ◽  
Crassostrea Corteziensis

The mangrove oysters (Crassostrea gasar) are molluscs native to the Amazonia region and their exploration and farming has increased considerably in recent years. These animals are farmed on beds built in the rivers of the Amazonia estuaries and, therefore, the composition of their microbiome should be directly influenced by environmental conditions. Our work aimed to evaluate the changes in bacterial composition of oyster's microbiota at two different seasons (rainy and dry). For this purpose, we amplified and sequenced the V3-V4 regions of the 16S rRNA gene. Sequencing was performed on the Illumina MiSeq platform. According to the rarefaction curve, the sampling effort was sufficient to describe the bacterial diversity in the samples. Alpha-diversity indexes showed that the bacterial microbiota of oysters is richer during the rainy season. This richness is possibly associated with the diversity at lower taxonomic levels, since the relative abundance of bacterial phyla in the two seasons remained relatively constant. The main phyla found include Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Similar results were found for the species Crassostrea gigas, Crassostrea sikamea, and Crassostrea corteziensis. Beta-diversity analysis showed that the bacterial composition of oyster's gut microbiota was quite different in the two seasons. Our data demonstrate the close relationship between the environment and the microbiome of these molluscs, reinforcing the need for conservation and sustainable management of estuaries in the Amazonia.

scholarly journals Alterations of the Gut Microbiome and Metabolome in Patients with Proliferative Diabetic Retinopathy

2020 ◽  
Author(s):  
Ke Yao ◽  
Panpan Ye ◽  
Xueyou Zhang ◽  
Yufeng Xu ◽  
Jia Xu ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Diabetic Patients ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Diagnostic Biomarkers ◽  
Rrna Gene Sequencing

Abstract Background: Diabetic retinopathy (DR) has been reported to associate with gut microbiota alterations in murine models and thus “gut-retina-axis” has been proposed. However, the role of gut microbiome and the associated metabolism in DR patients still need to be elucidated. Results: Fecal samples from 45 patients with proliferative DR (PDR) and 90 matched diabetic patients (1:2 according to age, sex and duration of diabetes) without DR (NDR) were subjected to 16S rRNA gene sequencing and untargeted metabolomics. Significantly lower bacterial diversity was observed in PDR group than that in NDR group. Differential gut bacterial composition was found, with significant depletion of 22 families (e.g., Coriobacteriaceae, Veillonellaceae and Streptococcaceae) and enrichment of 2 families (Burkholderiaceae and Burkholderiales_unclassified) in PDR group as compared to NDR group. There were significantly different fecal metabolic features, which were enriched in metabolic pathways such as arachidonic acid and microbial metabolism, between the two groups. Among 36 co-abundance metabolite clusters, 11 were positively/negatively contributed to PDR using logistic regression analysis. Fifteen gut microbial families were significantly correlated with the 11 metabolite clusters. Furthermore, a fecal metabolites-based classifier was constructed to distinguish PDR patients from NDR patients accurately.Conclusions: PDR is associated with reduced diversity and altered composition of gut microbiota and specific microbe-metabolite interplay. Our findings help to better understand the disease pathogenesis and provide novel diagnostic biomarkers and therapeutic targets for PDR.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 &#181;mol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Diversity, Composition and Functional Inference of Gut Microbiota in Indian Cabbage white Pieris canidia (Lepidoptera: Pieridae)

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 254
Author(s):  
Ying Wang ◽  
Jianqing Zhu ◽  
Jie Fang ◽  
Li Shen ◽  
Shuojia Ma ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Adult Survival ◽  
Rrna Gene ◽  
Life Stages ◽  
Microbial Composition ◽  
Significant Difference ◽  
Functional Inference ◽  
Rrna Gene Sequencing ◽  
Insect Fitness

We characterized the gut microbial composition and relative abundance of gut bacteria in the larvae and adults of Pieris canidia by 16S rRNA gene sequencing. The gut microbiota structure was similar across the life stages and sexes. The comparative functional analysis on P. canidia bacterial communities with PICRUSt showed the enrichment of several pathways including those for energy metabolism, immune system, digestive system, xenobiotics biodegradation, transport, cell growth and death. The parameters often used as a proxy of insect fitness (development time, pupation rate, emergence rate, adult survival rate and weight of 5th instars larvae) showed a significant difference between treatment group and untreated group and point to potential fitness advantages with the gut microbiomes in P. canidia. These data provide an overall view of the bacterial community across the life stages and sexes in P. canidia.

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