Recovery of temporary pond alpha and beta diversity after wildfire disturbance: the role of dispersal and recolonization processes

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).

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The lung microbiota in Korean patients with non-tuberculous mycobacterial pulmonary disease

BMC Microbiology ◽

10.1186/s12866-021-02141-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Sung-Yoon Kang ◽

Hyojung Kim ◽

Sungwon Jung ◽

Sang Min Lee ◽

Sang Pyo Lee

Keyword(s):

Principal Component Analysis ◽

Respiratory Tract ◽

Pulmonary Disease ◽

Beta Diversity ◽

Lower Respiratory Tract ◽

Principal Component ◽

Control Group ◽

Flexible Bronchoscope ◽

Bronchial Washing

Abstract Background The microbiota of the lower respiratory tract in patients with non-tuberculous mycobacterial pulmonary disease (NTM-PD) has not been fully evaluated. We explored the role of the lung microbiota in NTM-PD by analyzing protected specimen brushing (PSB) and bronchial washing samples from patients with NTM-PD obtained using a flexible bronchoscope. Results Bronchial washing and PSB samples from the NTM-PD group tended to have fewer OTUs and lower Chao1 richness values compared with those from the control group. In both bronchial washing and PSB samples, beta diversity was significantly lower in the NTM-PD group than in the control group (P = 2.25E-6 and P = 4.13E-4, respectively). Principal component analysis showed that the PSBs and bronchial washings exhibited similar patterns within each group but differed between the two groups. The volcano plots indicated differences in several phyla and genera between the two groups. Conclusions The lower respiratory tract of patients with NTM-PD has a unique microbiota distribution that is low in richness/diversity.

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The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽

10.3390/ani11030745 ◽

2021 ◽

Vol 11 (3) ◽

pp. 745

Author(s):

Michelle Martin de Bustamante ◽

Diego Gomez ◽

Jennifer MacNicol ◽

Ralph Hamor ◽

Caryn Plummer

Keyword(s):

Beta Diversity ◽

High Throughput Sequencing ◽

Illumina Miseq ◽

Diversity Indices ◽

Rrna Gene ◽

Linear Discriminant ◽

Alpha And Beta Diversity ◽

Bacterial Microbiota ◽

Healthy Control ◽

Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

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Partitioning tree diversity patterns to prioritize conservation investments

Environmental Conservation ◽

10.1017/s0376892921000060 ◽

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.

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The role of environmental conditions, climatic factors and spatial processes in driving multiple facets of stream macroinvertebrate beta diversity in a climatically heterogeneous mountain region

Ecological Indicators ◽

10.1016/j.ecolind.2021.107407 ◽

2021 ◽

Vol 124 ◽

pp. 107407

Author(s):

Xiaoming Jiang ◽

Baozhu Pan ◽

Wanxiang Jiang ◽

Yiming Hou ◽

Haiqiang Yang ◽

...

Keyword(s):

Environmental Conditions ◽

Beta Diversity ◽

Climatic Factors ◽

Mountain Region ◽

Spatial Processes ◽

Stream Macroinvertebrate

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Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽

10.3390/pathogens9060463 ◽

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.

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

International Journal of Biomathematics ◽

10.1142/s1793524515500114 ◽

2015 ◽

Vol 08 (01) ◽

pp. 1550011 ◽

Cited By ~ 3

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.

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