scholarly journals Historical signatures in the alpha and beta diversity patterns of Atlantic Forest harvestman communities (Arachnida: Opiliones)

2019 ◽  
Vol 97 (7) ◽  
pp. 631-643 ◽  
Author(s):  
A.A. Nogueira ◽  
C. Bragagnolo ◽  
M.B. DaSilva ◽  
T.K. Martins ◽  
E.P. Lorenzo ◽  
...  
Keyword(s):  
Protected Areas ◽  
Atlantic Forest ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Influential Factor ◽  
Conservation Strategies ◽  
Diversity Patterns ◽  
Alpha And Beta Diversity ◽  
Historical Factors ◽  
Compositional Changes

The integration of ecology and historical biogeography is fostering the investigation of diversity patterns. We studied alpha and beta diversity patterns of Brazilian Atlantic Forest harvestman (Arachnida: Opiliones) communities and related them to environmental and historical factors. Our data bank contains 508 species from 63 sites, encompassing almost the entire latitudinal range of Atlantic Forest. Alpha diversity was higher in coastal sites in the south and southeast regions and decreased in sites inland, as well as in sites in the coastal northeast region, especially in northern Bahia state. Alpha diversity was positively influenced by precipitation and altitudinal range, but the low number of species in northeastern coastal sites seems to be more related to the historical distribution of Neotropical harvestman lineages than to recent environmental factors. Geographic distance was the most influential factor for beta diversity. Compositional changes were also remarkably congruent with areas of endemism delimited for Atlantic Forest harvestmen. The percentage of protected areas for each area of endemism was very unbalanced, and Espírito Santo and Pernambuco states were the least protected areas. The turnover process observed in the compositional changes indicates that conservation strategies should include as many reserves as possible because every community presents a unique set of species.

scholarly journals Robust, data-driven bioregionalizations emerge from diversity concordance

2021 ◽  
Author(s):  
Cristian S. Montalvo-Mancheno ◽  
Jessie Buettel ◽  
Stefania Ondei ◽  
Barry W. Brook
Keyword(s):  
Species Diversity ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Data Driven ◽  
Conservation Units ◽  
Conservation Action ◽  
Diversity Patterns ◽  
Alpha And Beta Diversity ◽  
Terrestrial Vertebrates ◽  
Site Diversity

Aim: Despite the increasing interest in developing new bioregionalizations and assessing the most widely accepted biogeographic frameworks, no study to date has sought to systematically define a system of small bioregions nested within larger ones that better reflect the distribution and patterns of biodiversity. Here, we examine how an algorithmic, data-driven model of diversity patterns can lead to an ecologically interpretable hierarchy of bioregions. Location: Australia. Time period: Present. Major taxa studied: Terrestrial vertebrates and vascular plants. Methods: We compiled information on the biophysical characteristics and species occupancy of Australia′s geographic conservation units (bioregions). Then, using cluster analysis to identify groupings of bioregions representing optimal discrete-species areas, we evaluated what a hierarchical bioregionalization system would look like when based empirically on the within- and between-site diversity patterns across taxa. Within an information-analytical framework, we then assessed the degree to which the World Wildlife Fund′s (WWF) biomes and ecoregions and our suite of discrete-species areas are spatially associated and compared those results among bioregionalization scenarios. Results: Information on biodiversity patterns captured was moderate for WWF′s biomes (50–58% for birds′ beta, and plants′ alpha and beta diversity, of optimal discrete areas, respectively) and ecoregions (additional 4–25%). Our plants and vertebrate optimal areas retained more information on alpha and beta diversity across taxa, with the two algorithmically derived biogeographic scenarios sharing 86.5% of their within- and between-site diversity information. Notably, discrete-species areas for beta diversity were parsimonious with respect to those for alpha diversity. Main conclusions: Nested systems of bioregions must systematically account for the variation of species diversity across taxa if biodiversity research and conservation action are to be most effective across multiple spatial or temporal planning scales. By demonstrating an algorithmic rather than subjective method for defining bioregionalizations using species-diversity concordances, which reliably reflects the distributional patterns of multiple taxa, this work offers a valuable new tool for systematic conservation planning.

scholarly journals Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9003
Author(s):  
Zhongwei Yin ◽  
Keping Sun ◽  
Aoqiang Li ◽  
Deyi Sun ◽  
Zhongle Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Beta Diversity ◽  
Redundancy Analysis ◽  
Transition Period ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Alpha And Beta Diversity ◽  
Compositional Changes ◽  
Gut Microbial Community ◽  
Host Development

Background The gut microbiota is closely linked to host development, diet and health and is influenced by both the host and the environment. Although many studies have focused on the dynamics of the gut microbiota during development in captive animals, few studies have focused on the dynamics of the gut microbiota during development in wild animals, especially for the order Chiroptera. Methods In this study, we characterized the gut microbiota of the wild Asian particolored bat (Vespertilio sinensis) from 1 day to 6 weeks after birth. We explored the changes in their gut microbial community compositions, examined possible influencing factors, and predicted the feeding transition period. Results The gut microbiota changed during the development of V. sinensis. The alpha diversity of the bats’ gut microbiota gradually increased but did not change significantly from the 1st day to the 4th week after birth; however, the alpha diversity decreased significantly in week 5, then stabilized. The beta diversity differed slightly in weeks 4–6. In week 4, the fecal samples showed the highest diversity in bacterial community composition. Thus, we predicted that the potential feeding transition period for V. sinensis may occur during week 4. Redundancy analysis showed that age and body mass index significantly affected the compositional changes of the gut microbiota in Asian particolored bats. Conclusion The gut microbiota changed during the development of V. sinensis. We suggest that changes in the alpha and beta diversity during week 4 after birth indicate a potential feeding transition, highlighting the importance of diet in the gut microbiota during the development of V. sinensis.

scholarly journals Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

2021 ◽  
Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  
Keyword(s):  
Infant Formula ◽  
Beta Diversity ◽  
Milk Fat ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Term Infants ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).

Partitioning tree diversity patterns to prioritize conservation investments

2021 ◽  
pp. 1-9
Author(s):  
Patrick F McKenzie ◽  
Gwenllian D Iacona ◽  
Eric R Larson ◽  
Paul R Armsworth
Keyword(s):  
Protected Areas ◽  
Predictive Models ◽  
Tree Species ◽  
Beta Diversity ◽  
Distribution Data ◽  
Gamma Diversity ◽  
Conservation Practice ◽  
Alpha And Beta Diversity ◽  
Community Turnover ◽  
Data Limitations

Summary The available tools and approaches to inform conservation decisions commonly assume detailed distribution data. We examine how well-established ecological concepts about patterns in local richness and community turnover can help overcome data limitations when planning future protected areas. To inform our analyses, we surveyed tree species in protected areas in the southern Appalachian Mountains in the eastern USA. We used the survey data to construct predictive models for alpha and beta diversity based on readily observed biophysical variables and combined them to create a heuristic that could predict among-site richness in trees (gamma diversity). The predictive models suggest that site elevation and latitude in this montane system explain much of the variation in alpha and beta diversity in tree species. We tested how well resulting protected areas would represent species if a conservation planner lacking detailed species inventories for candidate sites were to rely only on our alpha, beta and gamma diversity predictions. Our approach selected sites that, when aggregated, covered a large proportion of the overall species pool. The combined gamma diversity models performed even better when we also accounted for the cost of protecting sites. Our results demonstrate that classic community biogeography concepts remain highly relevant to conservation practice today.

scholarly journals Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 463
Author(s):  
Mariusz Sikora ◽  
Albert Stec ◽  
Magdalena Chrabaszcz ◽  
Aleksandra Knot ◽  
Anna Waskiel-Burnat ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Large Scale ◽  
Skin Diseases ◽  
Intestinal Barrier ◽  
Alpha Diversity ◽  
Current Data ◽  
Intestinal Microbiome ◽  
Microbial Composition ◽  
Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

scholarly journals AB1232 ORAL DYSBIOSIS REFLECTS THE IMMUNOLOGICAL ALTERATION OF RA REGARDING TO ACPA AND HLA DRB1*SE: NAGASAKI ISLAND STUDY

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1907.2-1907
Author(s):  
Y. Tsuji ◽  
M. Tamai ◽  
S. Morimoto ◽  
D. Sasaki ◽  
M. Nagayoshi ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Healthy Subjects ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Unifrac Distance ◽  
Alpha And Beta Diversity ◽  
The Difference

Background:Anti-citrullinated protein antibody (ACPA) production is observed in several organs even prior to the onset of rheumatoid arthritis (RA), and oral mucosa is considered to be one of the important tissues. The presence of HLA-DRB1*SE closely associates with ACPA production. Saliva is considered to reflect the oral microbiota including periodontal disease. Alteration of oral microbiota of RA becomes to be normalized by DMARDs treatment, however, the interaction of HLA-DRB1*SE, ACPA and oral microbiota of RA patients remains to be elucidated.Objectives:The Nagasaki Island Study, which had started in 2014 collaborating with Goto City, is intended for research of the preclinical stage of RA, including ACPA/HLA genotype screening and ultrasound and magnetic resonance imaging examinations in high-risk subjects. Using the samples accumulated in this cohort, we have tried to investigate the difference of oral microbiota among RA patients and healthy subjects regarding to ACPA and HLA-DRB1*SE.Methods:Blood and salivary samples were obtained from 1422 subjects out of 4276 who have participated in the Nagasaki Island Study from 2016 to 2018. ACPA positivity was 1.7 % in total. Some of RA patients resided in Goto City participated in the Nagasaki Island Study. At this point, we selected 291 subjects, who were ACPA positive non-RA healthy subjects (n=22) and patients with RA (n=33, 11 subjects were ACPA positive and 22 ACPA negative respectively) as the case, age and gender matched ACPA negative non-RA healthy subjects (n=236) as the control. ACPA was measured by an enzyme-linked immunosorbent assay, and HLA genotyping was quantified by next-generation sequencing (Ref.1). The operational taxonomic unit (OUT) analysis using 16S rRNA gene sequencing were performed. The richness of microbial diversity within-subject (alpha diversity) was scaled via Shannon entropy. The dissimilarity between microbial community composition was calculated using Bray-Curtis distance as a scale, and differences between groups (beta diversity) were tested by permutational multivariate analysis of variance (PERMANOVA). In addition, UniFrac distance calculated in consideration of the distance on the phylogenetic tree were performed.Results:Median age 70 y.o., % Female 58.8 %. Among RA and non-RA subjects, not alpha diversity but beta diversity was statistically significance (p=0.022, small in RA). In RA subjects, both alpha and beta diversity is small (p<0.0001), especially significant in ACPA positive RA (Figure 1). Amongt RA subjects, presence of HLA-DRB1*SE did not show the difference but the tendency of being small of alpha diversity (p=0.29).Conclusion:Our study has suggested for the first time the association of oral microbiota alteration with the presence of ACPA and HLA-DRB1*SE. Oral dysbiosis may reflect the immunological status of patients with RA.References:[1]Kawaguchi S, et al. Methods Mol Biol 2018;1802: 22Disclosure of Interests:None declared

scholarly journals Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

2021 ◽  
Vol 9 (11) ◽  
pp. 2339
Author(s):  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Aleksandr G. Pinaev ◽  
Nikolay A. Provorov ◽  
Evgeny E. Andronov
Keyword(s):  
Microbial Communities ◽  
Plant Communities ◽  
Plant Diversity ◽  
Beta Diversity ◽  
Mutual Influence ◽  
Plant Root ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

Impact of intrapartum antibiotics on the infant gastrointestinal microbiome: a narrative review

2021 ◽  
pp. archdischild-2021-322590
Author(s):  
Laura Diamond ◽  
Rachel Wine ◽  
Shaun K Morris
Keyword(s):  
Gestational Age ◽  
Beta Diversity ◽  
Mode Of Delivery ◽  
Alpha Diversity ◽  
First Year ◽  
Feeding Method ◽  
Alpha And Beta Diversity ◽  
Ovid Medline ◽  
First Year Of Life ◽  
The Impact

BackgroundThe composition of the infant gastrointestinal (GI) microbiome has been linked to adverse long-term health outcomes and neonatal sepsis. Several factors are known to impact the composition of the microbiome, including mode of delivery, gestational age, feeding method and exposure to antibiotics. The impact of intrapartum antibiotics (IPAs) on the infant microbiome requires further research.ObjectiveWe aimed to evaluate the impact of IPAs on the infant GI microbiome.MethodsWe searched Ovid MEDLINE and Embase Classic+Embase for articles in English reporting on the microbiome of infants exposed to IPAs from the date of inception to 3 January 2021. Primary outcomes included abundance and colonisation of Bifidobacterium and Lactobacillus, as well as alpha and beta diversity.Results30 papers were included in this review. In the first year of life, following exposure to IPAs, 30% (6/20) of infant cohorts displayed significantly reduced Bifidobacterium, 89% (17/19) did not display any significant differences in Lactobacillus colonisation, 21% (7/34) displayed significantly reduced alpha diversity and 35% (12/34) displayed alterations in beta diversity. Results were further stratified by delivery, gestational age (preterm or full term) and feeding method.ConclusionsIPAs impact the composition of the infant GI microbiome, resulting in possible reductions Bifidobacterium and alpha diversity, and possible alterations in beta diversity. Our findings may have implications for maternal and neonatal health, including interventions to prevent reductions in health-promoting bacteria (eg, probiotics) and IPA class selection.

scholarly journals Evidence supporting the microbiota–gut–brain axis in a songbird

2020 ◽  
Vol 16 (11) ◽  
pp. 20200430
Author(s):  
Morgan C. Slevin ◽  
Jennifer L. Houtz ◽  
David J. Bradshaw ◽  
Rindy C. Anderson
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Cloacal Swab ◽  
Cognitive Tasks ◽  
Captive Population ◽  
Wild Populations ◽  
Alpha And Beta Diversity ◽  
Microbiome Research ◽  
Host Development

Recent research in mammals supports a link between cognitive ability and the gut microbiome, but little is known about this relationship in other taxa. In a captive population of 38 zebra finches ( Taeniopygia guttata ), we quantified performance on cognitive tasks measuring learning and memory. We sampled the gut microbiome via cloacal swab and quantified bacterial alpha and beta diversity. Performance on cognitive tasks related to beta diversity but not alpha diversity. We then identified differentially abundant genera influential in the beta diversity differences among cognitive performance categories. Though correlational, this study provides some of the first evidence of an avian microbiota–gut–brain axis, building foundations for future microbiome research in wild populations and during host development.

scholarly journals Unimodal Relationships of Understory Alpha and Beta Diversity along Chronosequence in Coppiced and Unmanaged Beech Forests

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 101 ◽  
Author(s):  
Sándor Bartha ◽  
Roberto Canullo ◽  
Stefano Chelli ◽  
Giandiego Campetella
Keyword(s):  
Beta Diversity ◽  
Management Practices ◽  
Multiple Scales ◽  
Forest Succession ◽  
Spatial Scales ◽  
Alpha Diversity ◽  
Structural Diversity ◽  
Diversity Indices ◽  
Alpha And Beta Diversity ◽  
Coppice Management

Patterns of diversity across spatial scales in forest successions are being overlooked, despite their importance for developing sustainable management practices. Here, we tested the recently proposed U-shaped biodiversity model of forest succession. A chronosequence of 11 stands spanning from 5 to 400 years since the last disturbance was used. Understory species presence was recorded along 200 m long transects of 20 × 20 cm quadrates. Alpha diversity (species richness, Shannon and Simpson diversity indices) and three types of beta diversity indices were assessed at multiple scales. Beta diversity was expressed by a) spatial compositional variability (number and diversity of species combinations), b) pairwise spatial turnover (between plots Sorensen, Jaccard, and Bray–Curtis dissimilarity), and c) spatial variability coefficients (CV% of alpha diversity measures). Our results supported the U-shaped model for both alpha and beta diversity. The strongest differences appeared between active and abandoned coppices. The maximum beta diversity emerged at characteristic scales of 2 m in young coppices and 10 m in later successional stages. We conclude that traditional coppice management maintains high structural diversity and heterogeneity in the understory. The similarly high beta diversities in active coppices and old-growth forests suggest the presence of microhabitats for specialist species of high conservation value.

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