scholarly journals Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12033
Author(s):  
Yi-ran Chen ◽  
Qin-long Jing ◽  
Fang-lan Chen ◽  
Huimin Zheng ◽  
Li-dan Chen ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Gut Microbiome ◽  
Large Scale ◽  
Community Diversity ◽  
Human Populations ◽  
Human Intestine ◽  
Adverse Health Effects ◽  
Waist Size ◽  
Host Health ◽  
The Relationship

Desulfovibrio (DSV) is frequently found in the human intestine but limited knowledge is available regarding the relationship between DSV and host health. In this study, we analyzed large-scale cohort data from the Guangdong Gut Microbiome Project to study the ecology of DSV and the associations of DSV and host health parameters. Phylogenetic analysis showed that Desulfovibrio piger might be the most common and abundant DSV species in the GGMP. Predominant sub-OTUs of DSV were positively associated with bacterial community diversity. The relative abundance of DSV was positively correlated with beneficial genera, including Oscillospira, Coprococcus,Ruminococcus,Akkermansia, Roseburia,Faecalibacterium, andBacteroides, and was negatively associated with harmful genera, such as Clostridium,Escherichia,Klebsiella, and Ralstonia. Moreover, the relative abundance of DSV was negatively correlated with body mass index, waist size, triglyceride levels, and uric acid levels. This suggests that DSV is associated with healthy hosts in some human populations.

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.

Analysis of microbial changes in the rhizosphere of unplanted and planted Atractylodes lancea via high-throughput sequencing

2020 ◽  
Author(s):  
Yan Xu ◽  
Junfeng Niu ◽  
Lijun Chen ◽  
Xiaoqiang Wu ◽  
Zhongmin Dong ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Relative Abundance ◽  
High Throughput Sequencing ◽  
Community Diversity ◽  
Continuous Cropping ◽  
Pests And Diseases ◽  
Atractylodes Lancea ◽  
Bacteria And Fungi ◽  
The Relationship

Abstract Background Atractylodes lancea is a traditional Chinese medicine, which typically requires more than 3–4 years of continuous cropping to obtain the underground medicinal components. With continuous cropping years, the quality and yields of A. lancea medicinal materials decrease, while pests and diseases increase. These aspects are intimately correlated with rhizospheric microorganisms. Methods This research paper employed high-throughput sequencing for its detection in soil that was cultivated for three years and never cultivated to clarify the relationship between the microbial diversity of the rhizosphere and continuous A. lancea cropping. Results The rhizosphere microbial community was altered following the continuous cropping of A. lancea. The bacterial diversity and richness were observed to decrease, while the fungal community diversity increased, and richness decreased. The total OUTs of the soil bacteria and fungi of unplanted and planted A. lancea were 59.58% and 37.65%, respectively. At the phylum level, the relative abundance of Proteobacteria, Gemmatimonadetes, Acidobacteria and Chloroflexi decreased, whereas the relative abundance of Mortierellomycota increased. At the genus level, Bradyrhizobium, Striaticonidium, Dactylonectria, Sphingomonas, Burkholderiaceae, Rhodanobacter, Arthrobacter, Scleroderma, Mortierella and Penicillium were significantly different between the two sample groups. Conclusions Our results revealed that following the cultivation of A. lancea, the rhizospheric microbial community was altered. This study preliminarily determined the

scholarly journals Rubidium chloride modulated the fecal microbiota community in mice

2020 ◽  
Author(s):  
Qian Chen ◽  
Zhiguo He ◽  
Yuting Zhuo ◽  
Shuzhen Li ◽  
Wenjing Yang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Fecal Microbiota ◽  
Community Diversity ◽  
Microbial Composition ◽  
Sulfate Reducing ◽  
Host Health ◽  
Bacterial Microbiome ◽  
Reducing Bacteria ◽  
First Time ◽  
The Relationship

Abstract Background: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study for depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated of their characteristics and bacterial microbiome changes.Results: The 16S ribosomal RNA gene sequencing of feces showed RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure for the first time. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio. While, RbCl significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. Besides, with regarding to the composition of archaea, RbCl significantly enhanced the abundances of Crenarchaeota, Thermoprotei, Sulfolobales, Sulfolobaceae and Sulfolobus lineages. Conclusions: These results revealed that enrichments of Clostridium XlVa and Alistipes could affect the levels of serotonin, a critical signaling molecule of brain-gut-microbiota axis. Therefore, anticancer and anti-depressant effects of RbCl might be partly mediated by modifying brain-gut-microbiota axis.

scholarly journals Rubidium chloride modulated the fecal microbiota community in mice

2020 ◽  
Author(s):  
Qian Chen ◽  
Zhiguo He ◽  
Yuting Zhuo ◽  
Shuzhen Li ◽  
Wenjing Yang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Fecal Microbiota ◽  
Community Diversity ◽  
Microbial Composition ◽  
Sulfate Reducing ◽  
16S Ribosomal Rna Gene ◽  
Host Health ◽  
Bacterial Microbiome ◽  
Reducing Bacteria ◽  
The Relationship

Abstract Background: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes.Results: The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level.Conclusions: Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention.

scholarly journals Rubidium chloride modulated the fecal microbiota community in mice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qian Chen ◽  
Zhiguo He ◽  
Yuting Zhuo ◽  
Shuzhen Li ◽  
Wenjing Yang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Fecal Microbiota ◽  
Community Diversity ◽  
Microbial Composition ◽  
Sulfate Reducing ◽  
16S Ribosomal Rna Gene ◽  
Host Health ◽  
Bacterial Microbiome ◽  
Reducing Bacteria ◽  
The Relationship

Abstract Background The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes. Results The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio, but significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. With regarding to the archaea, we only observed two less richness archaea Sulfolobus and Acidiplasma at the genus level. Conclusions Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention.

scholarly journals The Gut Microbiome and Resistome of Healthy Volunteers are Restructured After Short Courses of Antibiotics

2020 ◽  
Vol 41 (S1) ◽  
pp. s5-s6
Author(s):  
Winston Anthony ◽  
Kimberley Sukhum ◽  
Candice Cass ◽  
Kimberly Reske ◽  
Sondra Seiler ◽  
...  
Keyword(s):  
Healthy Volunteers ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Community Diversity ◽  
Metabolic Profiles ◽  
Innate Resistance ◽  
Starting Point ◽  
Stool Samples ◽  
Stool Specimens ◽  
Short Courses

Background: Antimicrobial exposure is a significant risk factor for the development of antibiotic-resistant organisms (ARO); however, the depth and duration of this impact is not well described. The study goal is to define impact of antibiotics on the gut microbiome of healthy volunteers (HVs). Methods: HVs were randomized to receive either 5 days of levofloxacin (LVX), azithromycin (AZM), cefpodoxime (CPD), or AZM + CPD (Fig. 1). Stool samples were collected at 15 time points per patient before, during, and after antibiotics. Remnant stool samples from the microbiology laboratory were collected from patients admitted to the medical intensive care unit (MICU) as a comparison of the microbiome in a critically ill state. DNA was extracted from samples and was submitted for shotgun sequencing. Relative abundance, resistome, and metabolic pathway abundance of bacterial taxa were determined and statistical analysis conducted in R software. Results: In total, 289 stool specimens from 20 HVs, and 26 remnant stool specimens were obtained from patients admitted from the MICU (Fig. 1). Community diversity and richness decreased in the first week post-ABX for all HVs (P < .01). Linear discriminant analysis identified Bacteroides and Clostridium as taxonomic groups enriched after CPD, while AZM and LVX produced a relative abundance increase in diverse Firmicutes spp. Longitudinal tracking confirmed that after all antibiotics except LVX, HV microbiomes lost species diversity and shifted toward a state similar to that observed in MICU patients (Fig. 2). The gut microbiome of most HVs exhibited resiliency and returned to a higher diversity level similar to their starting point; however, 10% of HVs did not. Moreover, antibiotic-specific increases in resistance markers reveal innate resistance to β-lactams and macrolides within the gut microbiome of the HVs. Finally, HV microbiomes, which shifted toward a MICU-like taxonomic state, also clustered with microbial metabolic profiles from MICU patients.The HV microbial metabolic profiles were significantly enriched for important biosynthesis pathways producing chorismate and polysaccharides. MICU patient gut microbiomes were enriched for fatty acid regulation and quinolone biosynthesis, and for many degradation pathways important for different aspects of antibiotic resistance such as membrane integrity, alternative respiration, and antibiotic inactivation. Conclusions: Short courses of antibiotics can cause acute and chronic microbiome disruptions in HVs, as evidenced by decreased microbiome diversity and increases in specific innate resistance elements. These data support the need for antimicrobial stewardship to support rationale antibiotic use to prevent gut microbiome disruptions.Funding: CDC BAA 200-2016-91962Disclosures: None

scholarly journals Blood metabolome signature predicts gut microbiome α-diversity in health and disease

2019 ◽  
Author(s):  
Tomasz Wilmanski ◽  
Noa Rappaport ◽  
John C. Earls ◽  
Andrew T. Magis ◽  
Ohad Manor ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Gut Microbiome ◽  
Laboratory Tests ◽  
Clinical Laboratory ◽  
The Body ◽  
Community Diversity ◽  
Blood Metabolites ◽  
Α Diversity ◽  
Host Health ◽  
Host Physiology

AbstractDefining a ‘healthy’ gut microbiome has been a challenge in the absence of detailed information on both host health and microbiome composition. Here, we analyzed a multi-omics dataset from hundreds of individuals (discovery n=399, validation n=540) enrolled in a consumer scientific wellness program to identify robust associations between host physiology and gut microbiome structure. We attempted to predict gut microbiome α-diversity from nearly 1000 analytes measured from blood, including clinical laboratory tests, proteomics and metabolomics. While a broad panel of 77 standard clinical laboratory tests and a set of 263 proteins from blood could not accurately predict gut microbial α-diversity, we found that 45% of the variance in microbial community diversity was explained by a subset of 40 blood metabolites, many of microbial origin. This relationship between the host metabolome and gut microbiome α-diversity was very robust, persisting across disease conditions and antibiotics use. Several of these novel metabolic biomarkers of gut microbial diversity were previously associated with host health (e.g. cardiovascular disease risk, diabetes, and kidney function). A subset of 11 metabolites classified participants with potentially problematic low α-diversity (ROC AUC=0.88, Precision-Recall AUC=0.76). Relationships between host metabolites and α-diversity remained consistent across most of the Body Mass Index (BMI) spectrum, but were modified in extreme obesity (class II/III, but not class I), suggesting a significant metabolic shift. Out-of-sample prediction accuracy of α-diversity from the 40 identified blood metabolites in a validation cohort, whose microbiome samples were analyzed by a different vendor, confirmed the robust correspondence between gut microbiome structure and host physiology. Collectively, our results reveal a strong coupling between the human blood metabolome and gut microbial diversity, with implications for human health.

scholarly journals Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology

2021 ◽  
Vol 12 ◽  
Author(s):  
Robert W. P. Glowacki ◽  
Morgan J. Engelhart ◽  
Philip P. Ahern
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Human Microbiome ◽  
Model Systems ◽  
Wild Mice ◽  
Host Health ◽  
Host Physiology ◽  
The Impact

The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such “wild mice” therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.

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

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinyue Zhang ◽  
Linjing Shi ◽  
Ting Sun ◽  
Kun Guo ◽  
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.

Relationship between total plasma homocysteine and the risk of aneurysms – a meta-analysis

VASA ◽  
2020 ◽  
pp. 1-6
Author(s):  
Hanji Zhang ◽  
Dexin Yin ◽  
Yue Zhao ◽  
Yezhou Li ◽  
Dejiang Yao ◽  
...  
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Single Species ◽  
Total Plasma ◽  
Control Groups ◽  
Randomized Controlled ◽  
Randomized Controlled Studies ◽  
The Difference ◽  
The Relationship ◽  
Healthy Participants

Summary: Our meta-analysis focused on the relationship between homocysteine (Hcy) level and the incidence of aneurysms and looked at the relationship between smoking, hypertension and aneurysms. A systematic literature search of Pubmed, Web of Science, and Embase databases (up to March 31, 2020) resulted in the identification of 19 studies, including 2,629 aneurysm patients and 6,497 healthy participants. Combined analysis of the included studies showed that number of smoking, hypertension and hyperhomocysteinemia (HHcy) in aneurysm patients was higher than that in the control groups, and the total plasma Hcy level in aneurysm patients was also higher. These findings suggest that smoking, hypertension and HHcy may be risk factors for the development and progression of aneurysms. Although the heterogeneity of meta-analysis was significant, it was found that the heterogeneity might come from the difference between race and disease species through subgroup analysis. Large-scale randomized controlled studies of single species and single disease species are needed in the future to supplement the accuracy of the results.

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