scholarly journals Ecophylogenetics Reveals the Evolutionary Associations between Mammals and their Gut Microbiota

2017 ◽  
Author(s):  
Christopher A. Gaulke ◽  
Holly K. Arnold ◽  
Steven W. Kembel ◽  
James P. O’Dwyer ◽  
Thomas J. Sharpton
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Host Selection ◽  
Evolutionary History ◽  
Common Ancestry ◽  
Mammalian Evolution ◽  
Novel Approach ◽  
Ecological Redundancy ◽  
Microbial Taxonomy ◽  
The Relationship

AbstractA tantalizing hypothesis posits that mammals coevolved with their gut microbiota. Unfortunately, the limited resolution of microbial taxonomy hinders the exploration of this hypothesis and specifically challenges the discovery of gut microbes that are linked to mammalian evolution. To address this, we developed a novel approach that groups microbes into new, more meaningful taxonomic units based on their common ancestry and ecological redundancy. Treating mammalian lineages as different ecosystems, we quantified the distribution of these microbial taxa across mammals. Our analysis discovered monophyletic clades of gut bacteria that are unexpectedly prevalent, or conserved, across all mammals, as well as conserved clades that are exclusive to particular mammalian lineages. These clades often manifest phylogenetic patterns indicating that they are subject to selection. Lineage - specific changes in clade conservation, including a human-accelerated loss of conserved clades, suggest that mammalian evolution associates with a change in the selective regimes that act on gut microbiota. Collectively, these results point to the existence of microbes that possess traits that facilitate their dispersion or survival in the mammalian gut, possibly because they are subject to host selection. Ultimately, our analysis clarifies the relationship between the diversification of the gut microbiome and mammalian evolutionary history.

scholarly journals Ecophylogenetics Clarifies the Evolutionary Association between Mammals and Their Gut Microbiota

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Christopher A. Gaulke ◽  
Holly K. Arnold ◽  
Ian R. Humphreys ◽  
Steven W. Kembel ◽  
James P. O’Dwyer ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Mammalian Species ◽  
Mammalian Evolution ◽  
Gut Microbes ◽  
Core Set ◽  
Shared Ancestry ◽  
Microbial Taxonomy ◽  
Microbiome Data

ABSTRACTOur knowledge of how the gut microbiome relates to mammalian evolution benefits from the identification of gut microbial taxa that are unexpectedly prevalent or unexpectedly conserved across mammals. Such taxa enable experimental determination of the traits needed for such microbes to succeed as gut generalists, as well as those traits that impact mammalian fitness. However, the punctuated resolution of microbial taxonomy may limit our ability to detect conserved gut microbes, especially in cases in which broadly related microbial lineages possess shared traits that drive their apparent ubiquity across mammals. To advance the discovery of conserved mammalian gut microbes, we developed a novel ecophylogenetic approach to taxonomy that groups microbes into taxonomic units based on their shared ancestry and their common distribution across mammals. Applying this approach to previously generated gut microbiome data uncovered monophyletic clades of gut bacteria that are conserved across mammals. It also resolved microbial clades exclusive to and conserved among particular mammalian lineages. Conserved clades often manifest phylogenetic patterns, such as cophylogeny with their host, that indicate that they are subject to selective processes, such as host filtering. Moreover, this analysis identified variation in the rate at which mammals acquire or lose conserved microbial clades and resolved a human-accelerated loss of conserved clades. Collectively, the data from this study reveal mammalian gut microbiota that possess traits linked to mammalian phylogeny, point to the existence of a core set of microbes that comprise the mammalian gut microbiome, and clarify potential evolutionary or ecologic mechanisms driving the gut microbiome’s diversification throughout mammalian evolution.IMPORTANCEOur understanding of mammalian evolution has become microbiome-aware. While emerging research links mammalian biodiversity and the gut microbiome, we lack insight into which microbes potentially impact mammalian evolution. Microbes common to diverse mammalian species may be strong candidates, as their absence in the gut may affect how the microbiome functionally contributes to mammalian physiology to adversely affect fitness. Identifying such conserved gut microbes is thus important to ultimately assessing the microbiome’s potential role in mammalian evolution. To advance their discovery, we developed an approach that identifies ancestrally related groups of microbes that distribute across mammals in a way that indicates their collective conservation. These conserved clades are presumed to have evolved a trait in their ancestor that matters to their distribution across mammals and which has been retained among clade members. We found not only that such clades do exist among mammals but also that they appear to be subject to natural selection and characterize human evolution.

scholarly journals Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients

2021 ◽  
Author(s):  
Xinyue Zhang ◽  
Kun Guo ◽  
Linjing Shi ◽  
Ting Sun ◽  
Songmei Geng
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Interleukin 2 ◽  
Negative Relationship ◽  
Healthy Individuals ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
The Relationship

Abstract Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease.Results: We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the dialister. The relative abundance of Phascolarctobacterium and dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions: We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

scholarly journals The Emerging Role of the Gut Microbiome in the Cancer Response to Immune Checkpoint Inhibitors: A Narrative Review

2021 ◽  
Author(s):  
Ghada Araji ◽  
Julian Maamari ◽  
Fatima Ali Ahmad ◽  
Rana Zareef ◽  
Patrick Chaftari ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Immune Checkpoint ◽  
Immune Checkpoint Inhibitors ◽  
Checkpoint Inhibitors ◽  
Therapeutic Interventions ◽  
The Impact ◽  
The Relationship ◽  
Gut Microbiota Composition

ABSTRACT The discovery of immune checkpoint inhibitors (ICIs) has revolutionized the care of cancer patients. However, the response to ICI therapy exhibits substantial interindividual variability. Efforts have been directed to identify biomarkers that predict the clinical response to ICIs. In recent years, the gut microbiome has emerged as a critical player that influences the efficacy of immunotherapy. An increasing number of studies have suggested that the baseline composition of a patient's gut microbiota and its dysbiosis are correlated with the outcome of cancer immunotherapy. This review tackles the rapidly growing body of evidence evaluating the relationship between the gut microbiome and the response to ICI therapy. Additionally, this review highlights the impact of antibiotic-induced dysbiosis on ICI efficacy and discusses the possible therapeutic interventions to optimize the gut microbiota composition to augment immunotherapy efficacy.

scholarly journals Dysbiotic Gut Microbiota and Dysregulation of Cytokine Profile in Children and Teens With Autism Spectrum Disorder

2021 ◽  
Vol 15 ◽  
Author(s):  
Xia Cao ◽  
Kevin Liu ◽  
Jun Liu ◽  
Yen-Wenn Liu ◽  
Li Xu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Cytokines ◽  
Gut Microbiome ◽  
Plasma Levels ◽  
Autism Spectrum ◽  
Tnf Α ◽  
Healthy Control ◽  
Ifn Γ ◽  
The Relationship ◽  
Pro Inflammatory Cytokines

Inflammation and the gut-brain axis have been implicated in the pathogenesis of autism spectrum disorders (ASDs). To further understand the relationship between aberrant immune responses and dysbiotic features of the gut microbiome in ASD, we enrolled 45 ASD individuals and 41 healthy control subjects with ages ranging from 2 to 19 years. We found that ASD group subjects have significantly higher plasma levels of IL-2, IL-4, IL-5, IL-6, IL-10, TNF-α, TNF-β, and IFN-γ when compared to healthy controls (FDR-adjusted p < 0.05). The plasma levels of pro-inflammatory cytokines IFN-γ and IL-6 are found to be further associated with several largely pathogenic gut microbiota uniquely detected in subjects with ASD. Furthermore, the ASD gut microbiome is characterized by reduced levels of several beneficial microbiota, including Bacteroides (FDR-adjusted p < 0.01) and Lachnospiraceae (FDR-adjusted p < 0.001). Analysis of Lachnospiraceae family and genus level taxa suggested that relative abundances of such taxa are negatively correlated with pro-inflammatory signaling cytokines IFN-γ and IL-6, particularly in subjects with severe ASD as defined by CARS (p < 0.05). Several largely pathogenic genera are determined to be associated with the pro-inflammatory cytokines IFN-γ and IL-6 (FDR-adjusted p < 0.1). Additionally, IL-4 is significantly negatively correlated with CARS total score (p < 0.05). Based on such results, we propose that the association between the disturbances of specific cytokines and alterations in gut microbiota abundance observed in children and adolescents with ASD provides additional evidence on the induction of aberrant pro-inflammatory mechanisms in ASD and its early diagnosis.

scholarly journals Determining the association between fibromyalgia, the gut microbiome and its biomarkers: A systematic review

2020 ◽  
Author(s):  
Sharon Erdrich ◽  
Jason A Hawrelak ◽  
Stephen P Myers ◽  
Joanna E Harnett
Keyword(s):  
Systematic Review ◽  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Original Research ◽  
Gastrointestinal Microbiota ◽  
Research Reporting ◽  
Gut Dysfunction ◽  
Irritable Bowel ◽  
The Relationship

Abstract Background The association between fibromyalgia and irritable bowel syndrome is well-established. Alterations in the composition and diversity of the gut microbiome in irritable bowel syndrome have been reported, however, this association is poorly understood in fibromyalgia. Our aim was to summarise the research reporting on the gastrointestinal microbiome and its biomarkers in people with fibromyalgia.Methods A systematic review of published original research reporting on the gastrointestinal microbiota and its biomarkers in adults with a diagnosis of fibromyalgia was undertaken.Results From 4771 studies, 11 met our inclusion criteria and were separated into four main groups: papers reporting Helicobacter pylori ; other gut bacterial markers; metabolomics and other biomarkers, which included intestinal permeability and small intestinal bacterial overgrowth.Conclusion The results suggest there is a paucity of quality research in this area, with indications that the gut microbiota may play a role in fibromyalgia within the emerging field of the gut-musculoskeletal axis. Further investigations into the relationship between the gut microbiota, gut dysfunction and fibromyalgia are warranted.

scholarly journals Gut microbiome and serum metabolome alterations in isolated dystonia

2021 ◽  
Author(s):  
Yongfeng Hu ◽  
Ling yan Ma ◽  
Min Cheng ◽  
Bo Liu ◽  
Hua Pan ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Metagenomic Sequencing ◽  
Metabolome Analysis ◽  
Citrate Cycle ◽  
Microbial Dysbiosis ◽  
Α Diversity ◽  
Drug Naïve ◽  
Neurological Movement Disorder ◽  
The Relationship

Abstract Background Dystonia is a complex neurological movement disorder characterised by involuntary muscle contractions. The relationship between the gut microbiota and isolated dystonia remains poorly explored. Methods We collected faeces and blood samples to study the microbiome and the serum metabolome from a cohort of 57 drug-naïve isolated dystonia patients and 27 age- and environment-matched healthy individuals. We first sequenced the V4 regions of the 16S rDNA gene from all faeces samples. Further, we performed metagenomic sequencing of gut microbiome and non-targeted metabolomics profiling of serum from dystonia patients with significant dysbiosis. Results Gut microbial β-diversity was significantly different, with a more heterogeneous community structure among dystonia individuals than healthy controls, while no difference in α-diversity was found. Gut microbiota in dystonia patients was enriched with Blautia obeum, Dorea longicatena and Eubacterium hallii, but depleted with Bacteroides vulgatus and Bacteroides plebeius. Metagenomic sequencing revealed that genes related to the citrate cycle, vitamin B6 and glycan metabolism were less abundant in dystonia, while genes linked to purine and tryptophan biosynthesis were more abundant. Serum metabolome analysis revealed altered levels of tyrosine and glutamate. The integrative analysis of the gut microbiome and serum metabolomics identified dystonia-associated gut microbial species linked to changes in serum metabolites, reflecting the effect of the gut microbiome on metabolic activity in isolated dystonia. Conclusion This study is the first to reveal gut microbial dysbiosis in dystonia patients. Our findings identified previously unknown links between intestinal microbiota alterations, circulating amino acids and dystonia, providing new insight into the pathogenesis of isolated dystonia.

scholarly journals Psoriasis and Gut Microbiome—Current State of Art

2021 ◽  
Vol 22 (9) ◽  
pp. 4529
Author(s):  
Karina Polak ◽  
Beata Bergler-Czop ◽  
Michał Szczepanek ◽  
Kamila Wojciechowska ◽  
Aleksandra Frątczak ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Response To Treatment ◽  
Current State ◽  
Immune Mediated ◽  
Bowel Diseases ◽  
Triggering Factor ◽  
Inflammatory Bowel ◽  
The Relationship ◽  
Gut Microbiota Composition

Psoriasis is a chronic, immune-mediated inflammatory disease that affects around 125 million people worldwide. Several studies concerning the gut microbiota composition and its role in disease pathogenesis recently demonstrated significant alterations among psoriatic patients. Certain parameters such as Firmicutes/Bacteroidetes ratio or Psoriasis Microbiome Index were developed in order to distinguish between psoriatic and healthy individuals. The “leaky gut syndrome” and bacterial translocation is considered by some authors as a triggering factor for the onset of the disease, as it promotes chronic systemic inflammation. The alterations were also found to resemble those in inflammatory bowel diseases, obesity and certain cardiovascular diseases. Microbiota dysbiosis, depletion in SCFAs production, increased amount of produced TMAO, dysregulation of the pathways affecting the balance between lymphocytes populations seem to be the most significant findings concerning gut physiology in psoriatic patients. The gut microbiota may serve as a potential response-to-treatment biomarker in certain cases of biological treatment. Oral probiotics administration as well as fecal microbial transplantation were most reported in bringing health benefits to psoriatic patients. However, the issue of psoriatic bacterial gut composition, its role and healing potential needs further investigation. Here we reviewed the literature on the current state of the relationship between psoriasis and gut microbiome.

scholarly journals Gut microbiome dysbiosis alleviates the progression of osteoarthritis in mice

2020 ◽  
Vol 134 (23) ◽  
pp. 3159-3174
Author(s):  
Zhiyuan Guan ◽  
Jialin Jia ◽  
Chenggui Zhang ◽  
Tiantong Sun ◽  
Wang Zhang ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Joint Injury ◽  
Trabecular Thickness ◽  
Tnf Α ◽  
Factor Α ◽  
The Relationship ◽  
Gut Microbiota Dysbiosis

Abstract Gut microbiota dysbiosis has been studied under the pathological conditions of osteoarthritis (OA). However, the effect of antibiotic-induced gut flora dysbiosis on OA remains incompletely understood at present. Herein, we used a mouse (8 weeks) OA model of destabilization of the medial meniscus (DMM) and gut microbiome dysbiosis induced by antibiotic treatment with ampicillin and neomycin for 8 weeks. The results show that antibiotic-induced intestinal microbiota dysbiosis reduced the serum level of lipopolysaccharide (LPS) and the inflammatory response, such as suppression of the levels of tumour necrosis factor-α (TNF-α) and interleukin-6 (IL-6), which can lead to decreased matrix metalloprotease-13 (MMP-13) expression and improvement of OA after joint injury. In addition, trabecular thickness (Tb.Th) and osteophyte scores were increased significantly in antibiotic-induced male mice compared with female mice. We further used network correlation analysis to verify the effect of gut microbiota dysbiosis on OA. Therefore, the present study contributes to our understanding of the gut–joint axis in OA and reveals the relationship between the inflammatory response, sex and gut microbiota, which may provide new strategies to prevent the symptoms and long-term sequelae of OA. Conclusion: Our data showed that gut microbiome dysbiosis alleviates the progression of OA.

scholarly journals Persistence and reversibility of arsenic-induced gut microbiome and metabolome shifts in rats after 30-days recovery duration

2020 ◽  
Author(s):  
Xiaoyan Du ◽  
Jie Zhang ◽  
Karl-Werner Schramm ◽  
Qingyu Huang ◽  
Meiping Tian ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Arsenic Exposure ◽  
Male Rats ◽  
Recovery Duration ◽  
Contaminated Drinking Water ◽  
Important Host ◽  
Novel Strategy ◽  
The Relationship

Abstract Background: The metabolites of gut microbiome are important host-health regulating factors and can be easily interrupted by the host exposure to environmental pollution via ingestion route. Arsenic contaminated drinking water is one of the most serious environmental problems worldwide. Therefore, the arsenic-induced alterations of gut microbiome and the metabolome, especially the persistence and reversibility parts of the alterations after the long-term arsenic exposure will be interesting to know. Results: We investigated the relationship between gut microbiota and its related metabolites in male rats both after the 30-days arsenic treatment and 30-days recovery duration. The composition and diversity of gut microbiota were affected significantly by the treatment, but they presented partial improvement in recovery duration. Moreover, arsenic exposure induced the significant changes of 73 metabolites, which involved in the metabolism of glycerophospholipid, linoleic acid, as well as the biosynthesis of phenylalanine, tyrosine and tryptophan. Although it had a persistent effect, the restoration of glycerophospholipid metabolism was observed in the 30-days recovery. Integration analysis further correlated the arsenic impacting microbes with some important differential metabolites, but only Lactobacillus associated with the decreases of phosphatidylethanolamine(34:1) , 16alpha-hydroxydehydroepiandrosterone 3-sulfate, seryltryptophan and alanyltyrosine in the recovery. Lactobacillus strains have potential to work as protective agents against arsenic toxicity by restoring perturbed glycerophospholipid metabolism. Conclusions: Arsenic significantly modified gut microbiome and metabolome, but arsenic-induced disruptions of gut microbiome and metabolome are reversible to some extent after a 30-days recovery. The deeper understanding of correlation of altered gut microbiome and metabolome could be a novel strategy to combat arsenic-induced disease.

scholarly journals Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates

2020 ◽  
Author(s):  
Christopher A. Gaulke ◽  
Courtney R. Armour ◽  
Ian R. Humphreys ◽  
Laura M. Beaver ◽  
Carrie L. Barton ◽  
...  
Keyword(s):  
Animal Models ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Evolutionary History ◽  
Species Variation ◽  
Human Gut ◽  
Gut Microbes ◽  
Comparative Metagenomics ◽  
Biochemical Pathways ◽  
History Of

AbstractWhile recent research reveals that the gut microbiome drives vertebrate health, little is known about whether the mechanisms these microbes employ to interact with physiology are consistent across host species. To help close this knowledge gap, we compared gut metagenomes across 10 vertebrate species, including biomedical animal models, to define the inter-species variation in the biochemical pathways encoded by gut microbiota. Doing so revealed gut-enriched pathways conserved across vertebrates, as well as pathways that vary concordantly with host evolutionary history. Overall, the functional capacity of the non-human gut microbiome generally reflects that of humans, though a subset of the pathways encoded by human gut microbiota are not well represented in non-human microbiomes. Collectively, these results support the use of animal models to study the mechanisms through which gut microbes impact human health, but suggest that researchers should cautiously consider which model will optimally represent a specific mechanism of interest.SignificanceEfforts to understand how the gut microbiome interacts with human physiology frequently relies on the use of animal models. However, it is generally not understood if the biochemical pathways encoded in gut microbiomes of these different animal models – which define the routes of interaction between gut microbes and their hosts – reflect those found in the human gut. To address this question, we compared gut metagenomes generated 10 different vertebrate lineages. In so doing, our study revealed that non-human gut metagenomes generally encode a set of pathways that are consistent with those found in the human gut. However, some human metagenome pathways are poorly represented in non-human guts, including pathways implicated in disease. Moreover, our analysis identified pathways that appear to be conserved across vertebrates, as well as pathways that are linked to the evolutionary history of their hosts, observations that hold potential to clarify the basis for phylosymbiosis.

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