Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment

Su, Xiaoquan

doi:10.1128/msystems.00363-21

Cited by 28 publications

(21 citation statements)

References 25 publications

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“…In the reviewed studies it was most often determined by using the Shannon index, but several measures are common for richness and evenness estimation, as the ACE-, Chao1-, and Simpson index, phylogenetic diversity, and the number of observed species [ 39 ]. Beta-diversity describes the difference between multiple samples and is mostly analyzed by using unweighted/weighted UniFrac distances and Bray-Curtis dissimilarity [ 40 ]. Additionally, PLS-DA (partial least squares discriminant analysis) was used to detect microbial patterns that separate depressed subjects from healthy controls (HC) [ 41 ].…”

Section: Resultsmentioning

confidence: 99%

The Role of the Gut Microbiota in the Development and Progression of Major Depressive and Bipolar Disorder

Knuesel

Mohajeri

2021

Nutrients

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A growing number of studies in rodents indicate a connection between the intestinal microbiota and the brain, but comprehensive human data is scarce. Here, we systematically reviewed human studies examining the connection between the intestinal microbiota and major depressive and bipolar disorder. In this review we discuss various changes in bacterial abundance, particularly on low taxonomic levels, in terms of a connection with the pathophysiology of major depressive and bipolar disorder, their use as a diagnostic and treatment response parameter, their health-promoting potential, as well as novel adjunctive treatment options. The diversity of the intestinal microbiota is mostly decreased in depressed subjects. A consistent elevation of phylum Actinobacteria, family Bifidobacteriaceae, and genus Bacteroides, and a reduction of family Ruminococcaceae, genus Faecalibacterium, and genus Roseburia was reported. Probiotics containing Bifidobacterium and/or Lactobacillus spp. seemed to improve depressive symptoms, and novel approaches with different probiotics and synbiotics showed promising results. Comparing twin studies, we report here that already with an elevated risk of developing depression, microbial changes towards a “depression-like” microbiota were found. Overall, these findings highlight the importance of the microbiota and the necessity for a better understanding of its changes contributing to depressive symptoms, potentially leading to new approaches to alleviate depressive symptoms via alterations of the gut microbiota.

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Section: Resultsmentioning

confidence: 99%

The Role of the Gut Microbiota in the Development and Progression of Major Depressive and Bipolar Disorder

Knuesel

Mohajeri

2021

Nutrients

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“…Normally, beta-diversity is measured by end-to-end comparison of microbiome pairs using distance metrics such as UniFrac or Bray–Curtis. Therefore, beta-diversity-based status identification and classification relies on an assumption that most members of the community, or at least the highly abundant members, are associated with the status of interest [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

Exploring the Potential of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 as Promising Psychobiotics Using SHIME

et al. 2023

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Psychobiotics are probiotics that have the characteristics of modulating central nervous system (CNS) functions or reconciled actions by the gut–brain axis (GBA) through neural, humoral and metabolic pathways to improve gastrointestinal activity as well as anxiolytic and even antidepressant abilities. The aim of this work was to evaluate the effect of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on the gut microbiota of mildly anxious adults using SHIME®. The protocol included a one-week control period and two weeks of treatment with L. helveticus R0052 and B. longum R0175. Ammonia (NH4+), short chain fatty acids (SCFAs), gamma-aminobutyric acid (GABA), cytokines and microbiota composition were determined. Probiotic strains decreased significantly throughout the gastric phase. The highest survival rates were exhibited by L. helveticus R0052 (81.58%; 77.22%) after the gastric and intestinal phase when compared to B. longum (68.80%; 64.64%). At the genus level, a taxonomic assignment performed in the ascending colon in the SHIME® model showed that probiotics (7 and 14 days) significantly (p < 0.005) increased the abundance of Lactobacillus and Olsenella and significantly decreased Lachnospira and Escheria-Shigella. The probiotic treatment (7 and 14 days) decreased (p < 0.001) NH4+ production when compared to the control period. For SCFAs, we observed after probiotic treatment (14 days) an increase (p < 0.001) in acetic acid production and total SCFAs when compared to the control period. Probiotic treatment increased (p < 0.001) the secretion of anti-inflammatory (IL-6 and IL-10) and decreased (p < 0.001) pro-inflammatory cytokines (TNF-alpha) when compared to the control period. The gut–brain axis plays an important role in the gut microbiota, producing SCFAs and GABA, stimulating the production of anti-anxiety homeostasis. The signature of the microbiota in anxiety disorders provides a promising direction for the prevention of mental illness and opens a new perspective for using the psychobiotic as a main actor of therapeutic targets.

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“…within alpha diversity: dominance, richness; within beta diversity: distance calculations methods, dimension reduction techniques, among others. For this purpose, metrics used to characterize these concepts, and the tools that allow their estimation, were proposed and developed inherited from other disciplines, such as the study of animal and plant communities, economics, sociology, or mining [17][18][19] and used practically without major distinctions [20][21][22] . Although these disciplines are based on information obtained through sampling, microbiota information has particular and speci c characteristics that requires special attention.…”

Section: Discussionmentioning

confidence: 99%

Unraveling Key Features of Microbial Alpha-Diversity Metrics and Their Practical Applications

Cassol

Ibañez

Bustamante

2023

Preprint

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Studies of microbial communities vary widely in terms of analysis methods. In this exponentially growing field, the wide variety of diversity measures and lack of consistency make it harder to compare different studies. Most existing alpha-diversity metrics are inherited from other disciplines and their assumptions are not always directly meaningful or true for microbiome data. Many existing microbiome studies apply one or some alpha diversity metrics with no fundamentals but also an unclear results interpretation. This work focuses on a theoretical, empirical, and comparative analysis of 19 frequently and less-frequently used microbial alpha-diversity metrics grouped into 4 proposed categories, including key features of every analyzed metric with their mathematical assumptions, in order to provide a deeper understanding of the existing metrics and a practical implementation guide for future studies.

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Elucidating the Beta-Diversity of the Microbiome: from Global Alignment to Local Alignment

Cited by 28 publications

References 25 publications

The Role of the Gut Microbiota in the Development and Progression of Major Depressive and Bipolar Disorder

The Role of the Gut Microbiota in the Development and Progression of Major Depressive and Bipolar Disorder

Exploring the Potential of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 as Promising Psychobiotics Using SHIME

Unraveling Key Features of Microbial Alpha-Diversity Metrics and Their Practical Applications

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