scholarly journals Box-Cox-chord transformations for community composition data prior to beta diversity analysis

Ecography ◽  
2018 ◽  
Vol 41 (11) ◽  
pp. 1820-1824 ◽  
Author(s):  
Pierre Legendre ◽  
Daniel Borcard
Keyword(s):  
Community Composition ◽  
Beta Diversity ◽  
Diversity Analysis ◽  
Composition Data

ANALYZING BETA DIVERSITY: PARTITIONING THE SPATIAL VARIATION OF COMMUNITY COMPOSITION DATA

2005 ◽  
Vol 75 (4) ◽  
pp. 435-450 ◽  
Author(s):  
Pierre Legendre ◽  
Daniel Borcard ◽  
Pedro R. Peres-Neto
Keyword(s):  
Spatial Variation ◽  
Community Composition ◽  
Beta Diversity ◽  
Diversity Partitioning ◽  
Composition Data

scholarly journals Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 27
Author(s):  
Hyo-Ryeon Kim ◽  
Jae-Hyun Lim ◽  
Ju-Hyoung Kim ◽  
Il-Nam Kim
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Marine Bacteria ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Composition Data ◽  
Decomposition Of Organic Matter ◽  
Class Level ◽  
Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

An island biogeography model for beta diversity and endemism: The roles of speciation, extinction and dispersal

2015 ◽  
Vol 08 (01) ◽  
pp. 1550011 ◽  
Author(s):  
Youhua Chen
Keyword(s):  
Numerical Simulation ◽  
Community Composition ◽  
Beta Diversity ◽  
Island Biogeography ◽  
Positive Relationship ◽  
Community Patterns ◽  
Speciation Rate ◽  
Immigration Rate ◽  
Extinction Rates

A community composition island biogeography model was developed to explain and predict two community patterns (beta diversity and endemism) with the consideration of speciation, extinction and dispersal processes. Results showed that rate of speciation is positively and linearly associated with beta diversity and endemism, that is, increasing species rates typically could increase the percentage of both endemism and beta diversity. The influences of immigration and extinction rates on beta diversity and endemism are nonlinear, but with numerical simulation, I could observe that increasing extinction rates would lead to decreasing percentage of endemism and beta diversity. The role of immigration rate is very similar to that of speciation rate, having a positive relationship with beta diversity and endemism. Finally, I found that beta diversity is closely related to the percentage of endemism. The slope of this positive relationship is determined jointly by different combinations of speciation, extinction and immigration rates.

Investigating the role of the gastrointestinal microbiome in response to immune checkpoint inhibitors (ICIs) among patients (pts) with metastatic renal cell carcinoma (mRCC).

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. 730-730 ◽  
Author(s):  
Anika Agarwal ◽  
Jennifer Modliszewski ◽  
Lauren Davey ◽  
Marco Reyes-Martinez ◽  
Daniella Runyambo ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Checkpoint Inhibitors ◽  
Predictive Biomarkers ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
P Value ◽  
Diversity Analysis ◽  
Microbial Composition ◽  
Response Factors ◽  
Microbial Dna

730 Background: ICIs are effective in mRCC, but one pertinent clinical need is to identify predictive biomarkers for response. The PD-1 receptor has been implicated in regulating gastrointestinal commensal bacteria, with varied immune interactions, thereby impacting response to ICIs. We evaluated bacterial taxa and ICI outcomes in mRCC pts. Methods: Fecal samples from 22 mRCC pts were collected at baseline, week (wk)-4 on ICI, and upon disease progression. Pts were grouped as responders (R, complete or partial response) or non-responders (NR, stable or progressive disease). Microbial DNA was isolated by next generation DNA sequencing. The V4 region of bacterial 16S ribosomal RNA was amplified from extracted DNA and analyzed for bacterial abundance, as well as alpha diversity indices (number of amplicon sequence variants [ASVs], Shannon’s Index, Faith’s Phylogenetic Diversity, and Pielou’s evenness) and beta diversity indices on ASVs (Bray-Curtis, Jaccard, and unweighted/weighted UniFrac dissimilarity measures). Results: Beta diversity analysis at baseline showed no difference in microbial composition between Rs and NRs. However, beta diversity analysis did show a significant change in composition from baseline to wk 4 in R vs NR pts (Bray Curtis p-value=0.03). Among mRCC pts with CR to ICIs, counts of bacteria in the phylum Verrucomicrobia had an upward trend from baseline to wk 4. All mRCC pts with CR (n=3) had Akkermansia at wk 4. However, Akkermansia colonization was not sufficient for response, present in 7/9 Rs and 6/11 NRs. Conclusions: Baseline microbiome differences between ICI Rs and NRs are not enough to predict outcomes. Diversity changes between baseline and wk-4 on treatment could be an early predictor of response. Factors other than presence of Akkermansia (tumor or host-specific, Akkermansia strain variation, or other bacteria in the microenvironment) may contribute to response. Further species and strain-level profiling of the microbiota, tumor-specific genomic alterations, host immune response, and increasing sample size of ICI-treated patients may improve detection of significant differences between Rs and NRs.

scholarly journals theseus - An R package for the analysis and visualization of microbial community data

2018 ◽  
Author(s):  
Jacob R. Price ◽  
Stephen Woloszynek ◽  
Gail Rosen ◽  
Christopher M. Sales
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Microbial Community Composition ◽  
R Package ◽  
Composition Data ◽  
Programming Framework ◽  
Community Data ◽  
R Programming

Abstracttheseus is a collection of functions within the R programming framework [1] to assist microbiologists and molecular biologists in the interpretation of microbial community composition data.

scholarly journals Degrees of compositional shift in tree communities vary along a gradient of temperature change rates over one decade: Application of an individual-based temporal beta-diversity concept

2020 ◽  
Author(s):  
Ryosuke Nakadai
Keyword(s):  
Temperature Change ◽  
Community Composition ◽  
Beta Diversity ◽  
Temporal Patterns ◽  
Diversity Indices ◽  
Temporal Changes ◽  
Individual Identity ◽  
Relative Speed ◽  
Identity Information ◽  
Temporal Beta Diversity

AbstractTemporal patterns in communities have gained widespread attention recently, to the extent that temporal changes in community composition are now termed “temporal beta-diversity”. Previous studies of beta-diversity have made use of two classes of dissimilarity indices: incidence-based (e.g., Sørensen and Jaccard dissimilarity) and abundance-based (e.g., Bray–Curtis and Ružička dissimilarity). However, in the context of temporal beta-diversity, the persistence of identical individuals and turnover among other individuals within the same species over time have not been considered, despite the fact that both will affect compositional changes in communities. To address this issue, I propose new index concepts for beta-diversity and the relative speed of compositional shifts in relation to individual turnover based on individual identity information. Individual-based beta-diversity indices are novel dissimilarity indices that consider individual identity information to quantitatively evaluate temporal change in individual turnover and community composition. I applied these new indices to individually tracked tree monitoring data in deciduous and evergreen broad-leaved forests across the Japanese archipelago with the objective of quantifying the effect of climate change trends (i.e., rates of change of both annual mean temperature and annual precipitation) on individual turnover and compositional shifts at each site. A new index explored the relative contributions of mortality and recruitment processes to temporal changes in community composition. Clear patterns emerged showing that an increase in the temperature change rate facilitated the relative contribution of mortality components. The relative speed of compositional shift increased with increasing temperature change rates in deciduous forests but decreased with increasing warming rates in evergreen forests. These new concepts provide a way to identify novel and high-resolution temporal patterns in communities.

scholarly journals Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration

2020 ◽  
Author(s):  
Rachel E. Cooper ◽  
Lisa M. Mangus ◽  
Jessica Lynch ◽  
Kayla Schonvisky ◽  
Justin R. Wright ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Beta Diversity ◽  
Rectal Swab ◽  
Bacterial Community Composition ◽  
16S Rrna Sequencing ◽  
Animal Origin ◽  
Common Marmosets ◽  
Rrna Sequencing

AbstractCharacterization of the gut microbiome may aid understanding and management of natural and experimental disease states in research animals, thereby promoting reproducibility. In this study, the rectal bacterial communities of three separate common marmoset (Callithrix jacchus) breeding colonies were defined using 16S rRNA sequencing of rectal swab samples. Study animals originated from two German colonies and a United States colony (JHU). The two German cohorts, previously fed the same diet, were imported into the JHU facility; they were then isolated, transitioned onto JHU diet, and then moved into rooms housing JHU animals. To dissect the contributions of diet and integration in shaping the rectal bacterial community, samples were collected from German origin marmosets upon JHU arrival (baseline), following diet transition (100 d), and following cohousing (390 d). Baseline and 390 d samples were collected from stably maintained JHU marmosets. Bacterial community composition was distinct between all three cohorts at baseline, suggesting that factors other than primary diet confer significant differences between captive populations. Beta-diversity of the animals from the two German colonies converged by 100 d but remained distinct from JHU sample beta-diversity throughout the 390-d study, indicating that diet had greater influence on bacterial community composition than did housing animals within the same room. Our results demonstrate substantial differences in gut bacteria between different captive marmoset colonies, with persistence of these differences following husbandry standardization and housing integration. Goals of rigor and reproducibility in research underscore the need to consider microbial differences between marmosets of diverse origin.ImportanceCharacterizing gut microbial populations is expected to promote health and enhance research reproducibility in animal studies. As use of common marmosets as animal models of human diseases expands, evaluating the marmoset gut bacterial community will be critical for interpreting research findings, especially as marmosets are prone to gastrointestinal inflammation. In this study, using 16S rRNA sequencing of rectal swab samples, we compared bacterial community among three captive colonies of marmosets at baseline and following importation of cohorts from two of the colonies into the third colony. Diet history had sustained influence on bacterial community composition, while housing the animals within the same room over a period of eight months did not appear to be a major factor. These persistent differences in marmoset gut bacterial community highlight the need for careful consideration of animal origin as a variable in marmoset research studies.

scholarly journals Individual-based multiple-unit dissimilarity: novel indices for assessing temporal variability in community composition

2021 ◽  
Author(s):  
Ryosuke Nakadai
Keyword(s):  
Community Composition ◽  
Beta Diversity ◽  
Temporal Dynamics ◽  
Diversity Indices ◽  
Barro Colorado Island ◽  
Forest Monitoring ◽  
List Type ◽  
Wide Range ◽  
Multiple Unit ◽  
Temporal Beta Diversity

AbstractBeta-diversity was originally defined spatially, i.e., as variation in community composition among sites in a region. However, the concept of beta-diversity has since been expanded to temporal contexts. This is referred to as “temporal beta-diversity”, and most approaches are simply an extension of spatial beta-diversity.The persistence and turnover of individuals over time is a unique feature of temporal beta-diversity. Nakadai (2020) introduced the “individual-based beta-diversity” concept, and provided novel indices to evaluate individual turnover and compositional shift by comparing individual turnover between two periods at a given site. However, the proposed individual-based indices are applicable only to pairwise dissimilarity, not to multiple-temporal (or more generally, multiple-unit) dissimilarity.Here, individual-based beta-diversity indices are extended to multiple-unit cases.To demonstrate the usage the properties of these indices compared to average pairwise measures, I applied them to a dataset for a permanent 50-ha forest dynamics plot on Barro Colorado Island in Panama.Information regarding “individuals” is generally missing from community ecology and biodiversity studies of temporal dynamics. In this context, the method proposed here is expected to be useful for addressing a wide range of research questions regarding temporal changes in biodiversity, especially studies using individual-tracked forest monitoring data.

scholarly journals Profiling the microbial community structure and functional diversity of a dam-regulated river undergoing gravel bar restoration

2020 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Bin Li ◽  
Tetsuya Sumi ◽  
Yasuhiro Takemon ◽  
Kozo Watanabe
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Beta Diversity ◽  
Environmental Heterogeneity ◽  
Trinity River ◽  
Metabolic Functions ◽  
Gravel Bars ◽  
Gravel Bar ◽  
The Trinity

AbstractBackgroundRiver restoration efforts are expected to influence and change the diversity and functions of microbial communities following the recovery of habitat characteristics in the river ecosystem. The recreation or restoration of gravel bars in the Trinity River in California aims to rehabilitate the environmental heterogeneity downstream of the dam impounded channel. Here, we profiled the community composition, estimated diversity, and annotated putative metabolic functions of the sediment microbial communities to assess whether the construction and restoration of gravel bars in the Trinity River in California enhanced environmental heterogeneity, with the increase in the microbial beta diversity of these in-channel structures against the free-flowing reach of the main channel with comparison to its undisturbed tributaries.ResultsMicrobial community composition of the free-flowing (i.e., no gravel bars) communities were relatively closer regardless of dam influence, whereas the Trinity River gravel bar and tributaries’ gravel bar communities were highly dissimilar. Proteobacteria, Bacteroidetes, and Acidobacteria were the highly abundant sediment microbial phyla on most sites, specifically in the Trinity River gravel bar communities. Putative functional annotation of microbial taxa revealed that chemoheterotrophy and aerobic chemoheterotrophy were the most prevalent microbial processes, with the Trinity River gravel bars having relatively higher representations. The considerably large abundance of heterotrophic taxa implies that gravel bars provide suitable areas for heterotrophic microorganisms with metabolic functions contributing to the net respiration in the river.ConclusionsOur results provide supporting evidence on the positive impact of habitat restoration being conducted in the Trinity River with the non-dam influenced, undisturbed tributaries as the basis of comparison. Gravel bar recreation and restoration contributed to the increased microbial biodiversity through the restoration of environmental heterogeneity at the river scale. We provided valuable insights into the potential microbial processes in the sediment that might be contributing to the biogeochemical processes carried out by the microbial communities in the Trinity River. The significant positive correlation between the functional diversity of the identified microbial taxa and beta diversity suggests that differences in the detected metabolic functions were closely related to dissimilarities in community composition.

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