scholarly journals Rarefaction, alpha diversity, and statistics

2017 ◽  
Author(s):  
Amy Willis
Keyword(s):  
Measurement Error ◽  
Microbial Diversity ◽  
Microbial Ecology ◽  
Ecosystem Function ◽  
Unknown Parameter ◽  
Alpha Diversity ◽  
Fundamental Question ◽  
Error Modeling ◽  
Extensive Literature ◽  
Statistical Methodology

AbstractUnderstanding the drivers of microbial diversity is a fundamental question in microbial ecology. Extensive literature discusses different methods for describing microbial diversity and documenting its effects on ecosystem function. However, it is widely believed that diversity depends on the number of reads that are sequenced. I discuss a statistical perspective on diversity, framing the diversity of an environment as an unknown parameter, and discussing the bias and variance of plug-in and rarefied estimates. I argue that by failing to account for both bias and variance, we invalidate analysis of alpha diversity. I describe the state of the statistical literature for addressing these problems, and suggest that measurement error modeling can address issues with variance, but bias corrections need to be utilized as well. I encourage microbial ecologists to avoid motivating their investigations with alpha diversity analyses that do not use valid statistical methodology.

scholarly journals Endocannabinoid system mediates the association between gut-microbial diversity and anhedonia/amotivation in a general population cohort

2021 ◽  
Author(s):  
Amedeo Minichino ◽  
Matthew A. Jackson ◽  
Marta Francesconi ◽  
Claire J. Steves ◽  
Cristina Menni ◽  
...  
Keyword(s):  
General Population ◽  
Microbial Diversity ◽  
Gut Microbiome ◽  
Endocannabinoid System ◽  
Alpha Diversity ◽  
Serum Levels ◽  
Population Cohort ◽  
Random Intercept ◽  
General Population Cohort ◽  
Antidepressant Use

AbstractAnhedonia and amotivation are debilitating symptoms and represent unmet therapeutic needs in a range of clinical conditions. The gut-microbiome-endocannabinoid axis might represent a potential modifiable target for interventions. Based on results obtained from animal models, we tested the hypothesis that the endocannabinoid system mediates the association between gut-microbiome diversity and anhedonia/amotivation in a general population cohort. We used longitudinal data collected from 786 volunteer twins recruited as part the TwinsUK register. Our hypothesis was tested with a multilevel mediation model using family structure as random intercept. The model was set using alpha diversity (within-individual gut-microbial diversity) as predictor, serum and faecal levels of the endocannabinoid palmitoylethanolamide (PEA) as mediator, and anhedonia/amotivation as outcome. PEA is considered the endogenous equivalent of cannabidiol, with increased serum levels believed to have anti-depressive effects, while increased stool PEA levels, reflecting increased excretion, are believed to have opposite, detrimental, effects on mental health. We therefore expected that either reduced serum PEA or increased stool PEA would mediate the association between microbial diversity and anhedonia amotivation. Analyses were adjusted for obesity, diet, antidepressant use, sociodemographic and technical covariates. Data were imputed using multiple imputation by chained equations. Mean age was 65.2 ± 7.6; 93% of the sample were females. We found a direct, significant, association between alpha diversity and anhedonia/amotivation (β = −0.37; 95%CI: −0.71 to −0.03; P = 0.03). Faecal, but not serum, levels of the endocannabinoid palmitoylethanolamide (PEA) mediated this association: the indirect effect was significant (β = −0.13; 95%CI: −0.24 to −0.01; P = 0.03), as was the total effect (β = −0.38; 95%CI: −0.72 to −0.04; P = 0.03), whereas the direct effect of alpha diversity on anhedonia/amotivation was attenuated fully (β = −0.25; 95%CI: −0.60 to 0.09; P = 0.16). Our results suggest that gut-microbial diversity might contribute to anhedonia/amotivation via the endocannabinoid system. These findings shed light on the biological underpinnings of anhedonia/amotivation and suggest the gut microbiota-endocannabinoid axis as a promising therapeutic target in an area of unmet clinical need.

scholarly journals Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation

2021 ◽  
Vol 9 (1) ◽  
pp. 100
Author(s):  
Alba C. Mayta-Apaza ◽  
Israel García-Cano ◽  
Konrad Dabrowski ◽  
Rafael Jiménez-Flores
Keyword(s):  
Microbial Diversity ◽  
Microbial Ecology ◽  
Illumina Miseq ◽  
Human Consumption ◽  
Fish Waste ◽  
Alpha And Beta Diversity ◽  
Analysis And Evaluation ◽  
Dynamic Variations ◽  
Acid Whey ◽  
By Products

The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals How Replicates Can Inform Potential Users of a Measurement Procedure about Measurement Error: Basic Concepts and Methods

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 162
Author(s):  
Werner Vach ◽  
Oke Gerke
Keyword(s):  
Measurement Error ◽  
Measurement Procedure ◽  
Statistical Methodology ◽  
Single Measurement ◽  
Conceptual Approach ◽  
Simple Manner ◽  
Scientific Investigations ◽  
Standard Procedures ◽  
Standardized Terminology ◽  
General Statistical

Measurement procedures are not error-free. Potential users of a measurement procedure need to know the expected magnitude of the measurement error in order to justify its use, in particular in health care settings. Gold standard procedures providing exact measurements for comparisons are often lacking. Consequently, scientific investigations of the measurement error are often based on using replicates. However, a standardized terminology (and partially also methodology) for such investigations is lacking. In this paper, we explain the basic conceptual approach of such investigations with minimal reference to existing terminology and describe the link to the existing general statistical methodology. This way, some of the key measures used in such investigations can be explained in a simple manner and some light can be shed on existing terminology. We encourage clearly conceptually distinguishing between investigations of the measurement error of a single measurement procedure and the comparison between different measurement procedures or observers. We also identify an unused potential for more advanced statistical analyses in scientific investigations of the measurement error.

Characterization of a PMU-based method for transmission line parameters estimation with systematic measurement error modeling

2021 ◽  
Author(s):  
Carlo Muscas ◽  
Paolo Attilio Pegoraro ◽  
Carlo Sitzia ◽  
Antonio Vincenzo Solinas ◽  
Sara Sulis ◽  
...  
Keyword(s):  
Measurement Error ◽  
Transmission Line ◽  
Error Modeling ◽  
Parameters Estimation ◽  
Systematic Measurement ◽  
Systematic Measurement Error

Microbial ecology of cereal vinegar fermentation: insights for driving the ecosystem function

2018 ◽  
Vol 49 ◽  
pp. 88-93 ◽  
Author(s):  
Zhen-Ming Lu ◽  
Zong-Min Wang ◽  
Xiao-Juan Zhang ◽  
Jian Mao ◽  
Jin-Song Shi ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Ecosystem Function

scholarly journals Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function

2017 ◽  
Vol 41 (2) ◽  
pp. 158-181 ◽  
Author(s):  
Lea Cabrol ◽  
Antonella Marone ◽  
Estela Tapia-Venegas ◽  
Jean-Philippe Steyer ◽  
Gonzalo Ruiz-Filippi ◽  
...  
Keyword(s):  
Microbial Ecology ◽  
Ecosystem Function ◽  
Fermentative Hydrogen

Microbial Diversity and Ecosystem Function

Oikos ◽  
1997 ◽  
Vol 80 (2) ◽  
pp. 209 ◽  
Author(s):  
Bland J. Finlay ◽  
Stephen C. Maberly ◽  
J. Ian Cooper
Keyword(s):  
Microbial Diversity ◽  
Ecosystem Function

scholarly journals From Microbial Ecology to Innovative Applications in Food Quality Improvements: the Case of Sourdough as a Model Matrix

J ◽  
2020 ◽  
Vol 3 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Mattia Pia Arena ◽  
Pasquale Russo ◽  
Giuseppe Spano ◽  
Vittorio Capozzi
Keyword(s):  
Microbial Diversity ◽  
Microbial Ecology ◽  
Scientific Community ◽  
Review Paper ◽  
Chemical Diversity ◽  
Fermented Foods ◽  
Quality Improvements ◽  
Model Matrix ◽  
Food And Beverage ◽  
Food Matrices

Since millennia, humankind has exploited microbial diversity associated to give food matrices in order to obtain fermented foods and beverages, resulting in products with improved quality and extended shelf life. This topic has received deserved and continuous interest in the scientific community, for the reason of its significance as a driver of innovation in the food and beverage sector. In this review paper, using sourdough as a model matrix, we provide some insights into the field, testifying the relevance as a transdisciplinary subject. Firstly, we encompassed the prokaryotic and eukaryotic microbial diversity associated with the sourdough ecosystems. The importance of this micro-biodiversity in the light of flour-related chemical diversity was examined. Finally, we highlighted the increasing interest in microbial-based applications oriented toward biocontrol solution in the field of sourdough-based products (i.e., bread).

scholarly journals Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Cui-Jing Zhang ◽  
Jie Pan ◽  
Chang-Hai Duan ◽  
Yong-Ming Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Alpha Diversity ◽  
Mean Annual Precipitation ◽  
Mangrove Sediments ◽  
Southeastern China ◽  
Deterministic Process ◽  
Deterministic Processes ◽  
Microbial Community Assembly

ABSTRACT Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms. IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

Sign in / Sign up

Export Citation Format

Share Document