scholarly journals Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

2020 ◽  
Author(s):  
Shawn P. Brown ◽  
Michael A. Grillo ◽  
Justin C. Podowski ◽  
Katy Denise Heath
Keyword(s):  
Medicago Truncatula ◽  
Root Nodule ◽  
Common Garden ◽  
Added Value ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Plant Genotype ◽  
Model Legume ◽  
Shotgun Metagenomic Sequencing ◽  
Soil Origin

Abstract Background: Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities.Results: Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment x soil origin and compartment x plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere.Conclusions: Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.

scholarly journals Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Shawn P. Brown ◽  
Michael A. Grillo ◽  
Justin C. Podowski ◽  
Katy D. Heath
Keyword(s):  
Medicago Truncatula ◽  
Root Nodule ◽  
Common Garden ◽  
Added Value ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Plant Genotype ◽  
Model Legume ◽  
Shotgun Metagenomic Sequencing ◽  
Soil Origin

Abstract Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Results Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless, all compartments were dominated by Ensifer, the genus of rhizobia that forms root nodule symbiosis with M. truncatula, and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Conclusions Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis toward a more mechanistic understanding of plant microbiomes.

scholarly journals Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

2020 ◽  
Author(s):  
Shawn P. Brown ◽  
Michael A. Grillo ◽  
Justin C. Podowski ◽  
Katy Denise Heath
Keyword(s):  
Medicago Truncatula ◽  
Root Nodule ◽  
Common Garden ◽  
Added Value ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Plant Genotype ◽  
Model Legume ◽  
Shotgun Metagenomic Sequencing ◽  
Soil Origin

Abstract Background Understanding the genetic and environmental factors that structure plant microbiomes is necessary for leveraging these interactions to address critical needs in agriculture, conservation, and sustainability. Legumes, which form root nodule symbioses with nitrogen-fixing rhizobia, have served as model plants for understanding the genetics and evolution of beneficial plant-microbe interactions for decades, and thus have added value as models of plant-microbiome interactions. Here we use a common garden experiment with 16S rRNA gene amplicon and shotgun metagenomic sequencing to study the drivers of microbiome diversity and composition in three genotypes of the model legume Medicago truncatula grown in two native soil communities. Results Bacterial diversity decreased between external (rhizosphere) and internal plant compartments (root endosphere, nodule endosphere, and leaf endosphere). Community composition was shaped by strong compartment × soil origin and compartment × plant genotype interactions, driven by significant soil origin effects in the rhizosphere and significant plant genotype effects in the root endosphere. Nevertheless all compartments were dominated by Ensifer , the genus of rhizobia that forms root nodule symbiosis with M. truncatula , and additional shotgun metagenomic sequencing suggests that the nodulating Ensifer were not genetically distinguishable from those elsewhere in the plant. We also identify a handful of OTUs that are common in nodule tissues, which are likely colonized from the root endosphere. Conclusions Our results demonstrate strong host filtering effects, with rhizospheres driven by soil origin and internal plant compartments driven by host genetics, and identify several key nodule-inhabiting taxa that coexist with rhizobia in the native range. Our results set the stage for future functional genetic experiments aimed at expanding our pairwise understanding of legume-rhizobium symbiosis towards a more mechanistic understanding of plant microbiomes.

scholarly journals Correction to: Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Shawn P. Brown ◽  
Michael A. Grillo ◽  
Justin C. Podowski ◽  
Katy D. Heath
Keyword(s):  
Medicago Truncatula ◽  
Plant Genotype ◽  
Model Legume ◽  
Soil Origin

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

scholarly journals Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients

2020 ◽  
Vol 4 (22) ◽  
pp. 5797-5809
Author(s):  
Emma E. Ilett ◽  
Mette Jørgensen ◽  
Marc Noguera-Julian ◽  
Jens Christian Nørgaard ◽  
Gedske Daugaard ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Diversity ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Clinical Factors ◽  
Hematopoietic Stem ◽  
Lower Abundance ◽  
Shotgun Metagenomic Sequencing ◽  
Stool Samples ◽  
Gene Richness

Abstract Acute graft-versus-host disease (aGVHD) is a leading cause of transplantation-related mortality after allogeneic hematopoietic stem cell transplantation (aHSCT). 16S ribosomal RNA (16S rRNA) gene-based studies have reported that lower gut bacterial diversity and the relative abundance of certain bacteria after aHSCT are associated with aGVHD. Using shotgun metagenomic sequencing and a large cohort, we aimed to confirm and extend these observations. Adult aHSCT recipients with stool samples collected from day −30 to day 100 relative to aHSCT were included. One sample was selected per patient per period (pre-aHSCT (day −30 to day 0), early post-aHSCT (day 1 to day 28), and late post-aHSCT (day 29 to day 100)), resulting in 150 aHSCT recipients and 259 samples. Microbial and clinical factors were tested for differences between time periods and an association with subsequent aGVHD. Patients showed a decline in gut bacterial diversity posttransplant, with several patients developing a dominance of Enterococcus. A total of 36 recipients developed aGVHD at a median of 34 days (interquartile range, 26-50 days) post-aHSCT. Lower microbial gene richness (P = .02), a lower abundance of the genus Blautia (P = .05), and a lower abundance of Akkermansia muciniphila (P = .01) early post-aHSCT was observed in those who developed aGVHD. Myeloablative conditioning was associated with aGVHD along with a reduction in gene richness and abundance of Blautia and A muciniphila. These results confirm low diversity and Blautia being associated with aGVHD. Crucially, we add that pretransplant conditioning is associated with changes in gut microbiota. Investigations are warranted to determine the interplay of gut microbiota and conditioning in the development of aGVHD.

scholarly journals Weaning age and its effect on the development of the swine gut microbiome and resistome

2021 ◽  
Author(s):  
Devin B Holman ◽  
Katherine E Gzyl ◽  
Kathy T Mou ◽  
Heather K Allen
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Carbohydrate Active Enzymes ◽  
Fecal Microbiome ◽  
Shotgun Metagenomic Sequencing ◽  
Swine Operations ◽  
Weaning Age

Piglets are often weaned between 19 and 22 d of age in North America although in some swine operations this may occur at 14 d or less. Piglets are abruptly separated from their sow at weaning and are quickly transitioned from sow's milk to a plant-based diet. The effect of weaning age on the long-term development of the pig gut microbiome is largely unknown. In this study, pigs were weaned at either 14, 21, or 28 d of age and fecal samples collected 21 times from d 4 (neonatal) through to marketing at d 140. The fecal microbiome was characterized using 16S rRNA gene and shotgun metagenomic sequencing. The fecal microbiome of all piglets shifted significantly three to seven days post-weaning with an increase in microbial diversity. Several Prevotella spp. increased in relative abundance immediately after weaning as did butyrate-producing species such as Butyricicoccus porcorum, Faecalibacterium prausnitzii, and Megasphaera elsdenii. Within 7 days of weaning, the gut microbiome of pigs weaned at 21 and 28 days of age resembled that of pigs weaned at 14 d. Resistance genes to most antimicrobial classes decreased in relative abundance post-weaning with the exception of those conferring resistance to tetracyclines and macrolides-lincosamides-streptogramin B. The relative abundance of microbial carbohydrate-active enzymes (CAZymes) changed significantly in the post-weaning period with an enrichment of CAZymes involved in degradation of plant-derived polysaccharides. These results demonstrate that pigs tend to have a more similar microbiome as they age and that weaning age has only a temporary effect on the gut microbiome.

scholarly journals Shedding light on biogas: a transparent reactor triggers the development of a biofilm dominated by Rhodopseudomonas faecalis that holds potential for improved biogas production

2019 ◽  
Author(s):  
Christian Abendroth ◽  
Adriel Latorre- Pérez ◽  
Manuel Porcar ◽  
Claudia Simeonov ◽  
Olaf Luschnig ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Biogas Production ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Nanopore Sequencing ◽  
Anaerobic Conditions ◽  
Complete Darkness ◽  
Anaerobic Digesters ◽  
Shotgun Metagenomic Sequencing ◽  
Effect Of Light

AbstractConventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on microbial communities operating in anaerobic digesters. In the present work, we have studied through 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a lab-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production. The biofilm proved surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out a photoautotroph metabolism when grown under anaerobic conditions. Our results suggest that this bacterium, able to fix carbon dioxide, could be considered for its use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH4:CO2 ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study supporting illuminated bioreactors as a new bioprocess for the obtention of biogas enriched in methane.

Foliar bacterial communities of trembling aspen in a common garden

2015 ◽  
Vol 61 (2) ◽  
pp. 143-149 ◽  
Author(s):  
Charles J. Mason ◽  
Jesse A. Pfammatter ◽  
Liza M. Holeski ◽  
Kenneth F. Raffa
Keyword(s):  
Bacterial Community ◽  
Host Plant ◽  
Bacterial Communities ◽  
Common Garden ◽  
Clonal Variation ◽  
Physical Factors ◽  
Rrna Gene ◽  
Trembling Aspen ◽  
Plant Genotype ◽  
Microbe Interactions

Microbial associations with plants are widely distributed and are structured by a number of biotic and physical factors. Among biotic factors, the host plant genotype may be integral to these plant–microbe interactions. Trees in the genus Populus have become models for studies in scaling effects of host plant genetics and in plant–microbe interactions. Using 454 pyrosequencing of the 16S rRNA gene, we assessed the foliar bacterial community of 7 genotypes of mature trembling aspen trees (Populus tremuloides Michx.) grown in a common garden. Trees were selected based on prior analyses showing clonal variation in their concentration of chemicals conferring resistance against insect herbivores. At broad taxonomic designations, the bacterial community of trembling aspen was similar across all plant genotypes. At a finer taxonomic scale, the foliage of these trees varied in their community composition, but there was no distinct pattern to colonization or abundance related to plant genotype. The most abundant operational taxonomic units (OTUs) were classified as Ralstonia, Bradyrhizobium, Pseudomonas, and Brucella. These OTUs varied across the common garden, but there was no significant effect of host plant genotype or spatial position on the abundance of these members. Our results suggest that aspen genotype is less important in the structuring of its foliar bacterial communities than are other, poorly understood processes.

scholarly journals Comparative analysis of 16S rRNA gene and metagenome sequencing in pediatric gut microbiomes

2021 ◽  
Author(s):  
Danielle Peterson ◽  
Kevin S. Bonham ◽  
Sophie Rowland ◽  
Cassandra W. Pattanayak ◽  
Vanja Klepac-Ceraj ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Gut Microbiome ◽  
Age Groups ◽  
Alpha Diversity ◽  
Sequencing Depth ◽  
Human Infant ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing

AbstractThe colonization of the human gut microbiome begins at birth, and, over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon versus shotgun metagenomic sequencing techniques in 130 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.

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