scholarly journals Persistence of functional microbiota composition across generations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Ramos ◽  
Mario Calus ◽  
Dirkjan Schokker
Keyword(s):  
Functional Traits ◽  
Host Species ◽  
Functional Composition ◽  
Interaction Patterns ◽  
Microbiota Composition ◽  
Interspecies Interaction ◽  
Units Of Selection ◽  
Pairwise Interactions ◽  
Over Time ◽  
Stable Community

AbstractHolobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The “it’s the song, not the singer” theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.

scholarly journals Persistence of Functional Microbiota Composition Across Generations

2020 ◽  
Author(s):  
Christian Ramos Uria ◽  
Mario Calus ◽  
Dirkjan Schokker
Keyword(s):  
Alternative Stable States ◽  
Simulated Data ◽  
Functional Composition ◽  
Interaction Patterns ◽  
Interspecies Interactions ◽  
Stable States ◽  
Units Of Selection ◽  
Pairwise Interactions ◽  
The Stability ◽  
Over Time

Abstract Background: Holobionts are defined as a host and its microbiota, and there is not a consensus about their status as a unit of selection. The “it’s the song, not the singer” theory proposes that functional traits, instead of taxonomical composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We used a novel combination of community level analysis on the functional composition of microbiota-communities to test this theory by using empirical and simulated data. We tested the conservation of functional composition across generations using mosquito and plant datasets. Then, we tested if there is a change of functional composition over time within a generation in human datasets. Finally, we simulated microbiota communities with different amounts of pairwise interspecies interactions and initial configurations to investigate if the interactions can lead to multiple stable community compositions. Results: Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time (i.e. an ecological succession) whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The pairwise interactions between species of the community are not sufficient to explain the stability of the final community and the existence of alternative stable states, which suggests that the host-microbiota interaction and non-pairwise interactions in general have an important contribution to the robustness of the final community.Conclusions: If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, suggesting this has a wider applicability, including animal breeding.

scholarly journals Higher-order temporal network effects through triplet evolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qing Yao ◽  
Bingsheng Chen ◽  
Tim S. Evans ◽  
Kim Christensen
Keyword(s):  
Real World ◽  
Link Prediction ◽  
Higher Order ◽  
Prediction Algorithm ◽  
Interaction Patterns ◽  
Temporal Networks ◽  
World Systems ◽  
Order Interaction ◽  
Space And Time ◽  
Pairwise Interactions

AbstractWe study the evolution of networks through ‘triplets’—three-node graphlets. We develop a method to compute a transition matrix to describe the evolution of triplets in temporal networks. To identify the importance of higher-order interactions in the evolution of networks, we compare both artificial and real-world data to a model based on pairwise interactions only. The significant differences between the computed matrix and the calculated matrix from the fitted parameters demonstrate that non-pairwise interactions exist for various real-world systems in space and time, such as our data sets. Furthermore, this also reveals that different patterns of higher-order interaction are involved in different real-world situations. To test our approach, we then use these transition matrices as the basis of a link prediction algorithm. We investigate our algorithm’s performance on four temporal networks, comparing our approach against ten other link prediction methods. Our results show that higher-order interactions in both space and time play a crucial role in the evolution of networks as we find our method, along with two other methods based on non-local interactions, give the best overall performance. The results also confirm the concept that the higher-order interaction patterns, i.e., triplet dynamics, can help us understand and predict the evolution of different real-world systems.

scholarly journals Canopy Leaf Traits, Basal Area, and Age Predict Functional Patterns of Regenerating Communities in Secondary Subtropical Forests

2021 ◽  
Vol 4 ◽  
Author(s):  
Sandra Cristina Müller ◽  
Rodrigo Scarton Bergamin ◽  
Kauane Maiara Bordin ◽  
Joice Klipel ◽  
Milena Fermina Rosenfield
Keyword(s):  
Functional Diversity ◽  
Functional Traits ◽  
Natural Regeneration ◽  
Basal Area ◽  
Leaf Traits ◽  
Leaf Nitrogen ◽  
Ecosystem Functions ◽  
Secondary Forests ◽  
Functional Composition ◽  
Forest Age

Secondary forests originate from natural regeneration after fallow (succession) or restoration. Species assembly in these communities, which can affect ecosystem functions and successional trajectories, is very unpredictable. Trait-based trajectories can shed light on the recovery of ecosystem functions and enable predictions of how the regenerating communities will change with forest age. Regeneration communities are affected by initial conditions and also by canopy structure and functional traits that alter dispersers' attractiveness and coexistence mechanisms. Here we evaluated how community functional traits change over time and tested if functional diversity and composition of the established canopy, as well as the structure of the canopy and forest age, influence the functional structure of regenerating tree communities when compared to their reference forests. For this, we calculated dissimilarity in trait composition (community-weighted means) and in functional diversity of regenerating communities of each succession/restoration stand, using the tree stratum of nearby mature forests as baseline values. Functional trait information comprises leaf, wood density, and reproductive traits from tree species. Our community data contain information from natural successional forests and restoration sites, in the South-Brazilian Atlantic Forest. Predictor variables of functional dissimilarities were forest age, canopy structural variables, canopy functional composition, and functional diversity. Results showed leaf traits (leaf dry matter content, leaf nitrogen content, leaf nitrogen-phosphorus ratio) and seed mass varying with forest age. Canopy functional composition based on leaf traits and total basal area significantly predicted multiple trait functional dissimilarity between the regeneration component of secondary forests and their reference community values. Dissimilarity increased when the canopy was composed of species with more acquisitive traits. Difference in functional diversity was only influenced by forest age. Mid-stage secondary forests showed lower functional diversity than early-stage forests. Our results indicated the importance of canopy traits on the natural regeneration of secondary subtropical forests. If functional similarity with reference forests is a desired objective in order to recover ecosystem functions through natural regeneration, leaf functional traits of canopy trees that establish or are planted in degraded areas must be considered in the successional processes.

scholarly journals Faecal Microbiota Dynamics and their Relation to Disease Course in Crohn’s Disease

2019 ◽  
Vol 13 (10) ◽  
pp. 1273-1282 ◽  
Author(s):  
Gianluca Galazzo ◽  
Danyta I Tedjo ◽  
Dion S J Wintjens ◽  
Paul H M Savelkoul ◽  
Ad A M Masclee ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Community Structure ◽  
Microbial Community ◽  
Disease Activity ◽  
Microbial Community Structure ◽  
Disease Course ◽  
Microbiota Composition ◽  
Faecal Microbiota ◽  
Over Time

Abstract Background Microbial shifts have been associated with disease activity in Crohn’s disease [CD], but findings on specific taxa are inconsistent. This may be due to differences in applied methods and cross-sectional study designs. We prospectively examined the faecal microbiota in adult CD patients with changing or stable disease course over time. Methods Faeces were collected at two time-points from 15 healthy control individuals [HCs], 35 CD patients who were in remission and who maintained remission [RRs], and 22 CD patients during remission and also during subsequent exacerbation [RAs]. The microbial composition was assessed by 16S rRNA [V4] gene sequencing. Results Compared with HCs, patients with CD had a lower microbial richness [p = 0.0002] and diversity [p = 0.005]. Moreover, the microbial community structure of a subset of patients, clustered apart from HCs, was characterized by low microbial diversity and Faecalibacterium abundance. Patients within this cluster did not differ with respect to long-term disease course compared with patients with a ‘healthy-appearing’ microbiota. Over time, microbial richness and diversity did not change in RR versus RA patients. Although the microbial community structure of both RR and RA patients was less stable over time compared with that of HCs, no differences were observed between the patient groups [p = 0.17]; nor was the stability impacted by Montreal classification, medication use, or surgery. Conclusion The altered microbiota composition and stability in CD was neither associated with disease activity nor long-term disease course, questioning its involvement in the development of an exacerbation. The aberrant microbiota composition in a subset of CD patients warrants further exploration of a more microbiota-driven etiology in this group.

scholarly journals Can plant functional traits explain shifts in community composition in a changing Arctic?

2021 ◽  
Author(s):  
Katlyn Rose Betway ◽  
Robert D. Hollister ◽  
Jeremy May ◽  
Jacob A. Harris ◽  
William Gould ◽  
...  
Keyword(s):  
Community Composition ◽  
Functional Traits ◽  
Ecosystem Functioning ◽  
Repeated Measures ◽  
Vascular Plant ◽  
Plant Cover ◽  
The Arctic ◽  
And Function ◽  
Northern Alaska ◽  
Over Time

The Arctic is warming more than twice the global average. Graminoids, deciduous shrubs, and evergreen shrubs have been shown to increase in cover in some regions, but not others. To better understand why plant response varies across regions, we compared change in cover over time with nine functional traits of twelve dominant species at three regions in northern Alaska (Utqiaġvik, Atqasuk, and Toolik Lake). Cover was measured three times from 2008 to 2018. Repeated measures ANOVA found one species showed a significant change in cover over time; Carex aquatilis increased at Atqasuk by 12.7%. Canonical correspondence analysis suggested a relationship between shifts in species cover and traits, but Pearson and Spearman correlations did not find a significant trend for any trait when analyzed individually. Investigation of community-weighted means (CWM) for each trait revealed no significant changes over time for any trait at any region. Whereas, estimated ecosystem values for several traits important to ecosystem functioning showed consistent increases over time at two regions (Utqiaġvik and Atqasuk). Results thus indicate that vascular plant community composition and function have remained consistent over time; however, documented increases in total plant cover have important implications for ecosystem functioning.

scholarly journals Pairwise Interactions of Three Related Pseudomonas Species in Plant Roots and Inert Surfaces

2021 ◽  
Vol 12 ◽  
Author(s):  
Nesli Tovi ◽  
Tomer Orevi ◽  
Maor Grinberg ◽  
Nadav Kashtan ◽  
Yitzhak Hadar ◽  
...  
Keyword(s):  
Bacterial Colonization ◽  
Plant Roots ◽  
Microbial Consortia ◽  
Root Tip ◽  
Interaction Patterns ◽  
Interspecies Interactions ◽  
Wheat Roots ◽  
Pairwise Interactions ◽  
Inert Surfaces ◽  
External Stimuli

Bacteria are social organisms that interact extensively within and between species while responding to external stimuli from their environments. Designing synthetic microbial communities can enable efficient and beneficial microbiome implementation in many areas. However, in order to design an efficient community, one must consider the interactions between their members. Using a reductionist approach, we examined pairwise interactions of three related Pseudomonas species in various microenvironments including plant roots and inert surfaces. Our results show that the step between monoculture and co-culture is already very complex. Monoculture root colonization patterns demonstrate that each isolate occupied a particular location on wheat roots, such as root tip, distance from the tip, or scattered along the root. However, pairwise colonization outcomes on the root did not follow the bacterial behavior in monoculture, suggesting various interaction patterns. In addition, we show that interspecies interactions on a microscale on inert surface take part in co-culture colonization and that the interactions are affected by the presence of root extracts and depend on its source. The understanding of interrelationships on the root may contribute to future attempts to manipulate and improve bacterial colonization and to intervene with root microbiomes to construct and design effective synthetic microbial consortia.

scholarly journals The urinary microbiota composition remains stable over time and under various storage conditions

2019 ◽  
Author(s):  
Caspar Bundgaard-Nielsen ◽  
Nadia Ammitzbøll ◽  
Yusuf Abdi Isse ◽  
Abdisalam Muqtar ◽  
Ann-Maria Jensen ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Study Design ◽  
Storage Conditions ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Male Adult ◽  
Bacterial Composition ◽  
Urinary Microbiota ◽  
Over Time

AbstractBackgroundNew sensitive techniques have revealed a large population of bacteria in the human urinary tract, challenging the perception of the urine of healthy humans being sterile. While the role of this urinary microbiota is unknown, dysbiosis has been linked to disorders like urgency urinary incontinence and interstitial cystitis. When comparing studies it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether storage condition or time of collection, had any impact on the urinary microbial composition.ResultsFor comparison of different storage conditions, urine was collected from five healthy adult female donors, and analyzed by 16S rRNA gene sequencing. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in nineteen healthy donors, including four women, five men, five girls, and five boys. With the exception of two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of the urinary microbiota was found to be highly resilient to changes introduced by storage temperature and duration. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys.Together our study supports flexibility in study design, when conducting urinary microbiota studies.Author summaryThe discovery of bacteria native to the urinary tract in healthy people, a location previously believed to be sterile, has prompted research into the clinical potential of these bacteria. However, methodological weaknesses can significantly influence such studies, and thus development of robust techniques for investigating these bacteria are needed. In the present study, we investigated whether differences in storage following collection, could affect the bacterial composition of urine samples. Next, we investigated if this composition exhibited daily or day-to-day variations.Firstly, we found, that the bacterial composition of urine could be maintained by storage at −80 °C, −20 °C, or refrigerated at 4 °C. Secondly, the bacterial composition of urine remained stable over time. Overall, the results of this study provide information important to study design in future investigations into the clinical implications of urinary bacteria.

scholarly journals Evolutionary History Impacts Phyllosphere Community Assembly on Forage Grasses

2021 ◽  
Author(s):  
Emily K. Bechtold ◽  
Klaus Nüsslein
Keyword(s):  
Drought Stress ◽  
Microbial Communities ◽  
Community Assembly ◽  
Host Species ◽  
Evolutionary History ◽  
Plant Traits ◽  
Evolutionary Relationship ◽  
Grass Species ◽  
Plant Hosts ◽  
Over Time

Benefits leaf bacterial communities provide to plant hosts are reduced by external stress. Understanding how plant hosts impact phyllosphere community assembly, how microbes influence plant traits, and how this interaction changes under stress will advance our insight into the evolutionary relationship between plants and their microbial communities. We investigated phyllosphere community assembly change over time, between host species, and under drought stress on three native temperate grasses and three non-native tropical grasses. By growing them together, effects of host geography and differences in environmental variables were eliminated allowing us to test evolutionary history on community assembly. We found evidence of phylosymbiosis which increased significantly under drought stress, indicating phyllosphere communities and their response to stress relate to grass species phylogeny. We also show native temperate grasses displayed stronger cophylogenetic relationships between grass hosts and their microbial communities and had increased selection by host species over time compared to non-native tropical hosts. Interestingly, the functional marker gene nifH, though differentially present on all host species was not susceptible to drought. The evidence of shared evolutionary history, presence of functionally important bacteria, and responses to drought suggest that microbial communities are important plant traits that coevolve alongside their plant hosts.

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