scholarly journals Alterations in the gut microbiota and metabolite profiles of patients with Kashin-Beck disease, an endemic osteoarthritis in China

2021 ◽  
Vol 12 (11) ◽  
Author(s):  
Xi Wang ◽  
Yujie Ning ◽  
Cheng Li ◽  
Yi Gong ◽  
Ruitian Huang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
Metabolic Networks ◽  
Unsaturated Fatty Acids ◽  
Abundant Species ◽  
Metagenomic Sequencing ◽  
Serum Samples ◽  
Genetic And Environmental Factors ◽  
Specific Species ◽  
Beck Disease

AbstractKashin-Beck disease (KBD) is a severe osteochondral disorder that may be driven by the interaction between genetic and environmental factors. We aimed to improve our understanding of the gut microbiota structure in KBD patients of different grades and the relationship between the gut microbiota and serum metabolites. Fecal and serum samples collected from KBD patients and normal controls (NCs) were used to characterize the gut microbiota using 16S rDNA gene and metabolomic sequencing via liquid chromatography-mass spectrometry (LC/MS). To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria in the KBD patients, metagenomic sequencing of fecal samples from grade I KBD, grade II KBD and NC subjects was performed. The KBD group was characterized by elevated levels of Fusobacteria and Bacteroidetes. A total of 56 genera were identified to be significantly differentially abundant between the two groups. The genera Alloprevotella, Robinsoniella, Megamonas, and Escherichia_Shigella were more abundant in the KBD group. Consistent with the 16S rDNA analysis at the genus level, most of the differentially abundant species in KBD subjects belonged to the genus Prevotella according to metagenomic sequencing. Serum metabolomic analysis identified some differentially abundant metabolites among the grade I and II KBD and NC groups that were involved in lipid metabolism metabolic networks, such as that for unsaturated fatty acids and glycerophospholipids. Furthermore, we found that these differences in metabolite levels were associated with altered abundances of specific species. Our study provides a comprehensive landscape of the gut microbiota and metabolites in KBD patients and provides substantial evidence of a novel interplay between the gut microbiome and metabolome in KBD pathogenesis.

scholarly journals Integrated Multi-Omics Data Analysis Reveals Altered Metabolome Activity and Microbiome Composition in Irritable Bowel Syndrome

2020 ◽  
Author(s):  
Xiaodong Fang ◽  
Lijuan Han ◽  
Ling Zhao ◽  
Yong Zhou ◽  
Chao Yang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Functional Gastrointestinal Disorders ◽  
Abundant Species ◽  
Fatty Acyl ◽  
Omics Data ◽  
Serum Samples ◽  
Serum Metabolites ◽  
Microbiome Composition ◽  
Irritable Bowel

Abstract Background: Irritable bowel syndrome (IBS) is one of functional gastrointestinal disorders mainly characterized by chronic and/or recurrent symptoms of abdominal pain and irregular defecation. Changed gut microbiota has been proposed to mediate IBS; however, contradictory results exist, and the exact mechanism is still debatable. IBS-specific microbiota and metabolite remain poorly understand. To address this issue, we performed untargeted metabolomic and shotgun metagenomic profiling of stool and serum samples from discovery (n=330) and validation (n=101) cohorts of IBS and healthy individuals. Results: Fecal “omics” data show moderate dysbiosis compared with other disease, in contrast, serum metabolites show significant differences and have great power to discriminate IBS from healthy subjects. Specifically, 726 differentially abundant serum metabolites are identified, including fatty acyl-CoA enriched in IBS. Integrating microbiome and metabolome data, we identified 522 robust associations between differentially abundant species and fecal metabolites, of which three species are strongly associated with the low abundance of dihydropteroic acid. Moreover, the tryptophan enrichment correlates with the severity of IBS depression in both fecal and serum metabolomes. Conclusions: Collectively, our study unveils serum/fecal metabolome alterations and their relationship with gut microbiome and highlight the massive dysbiosis of serum metabolites which empower to discriminate IBS patients. Our study also provides a valuable resource for future studies to understand host-gut microbiota relationships, and facilitate potential clinical applications using microbiota and (or) metabolites to evaluate IBS patients with depression.

scholarly journals Identification of the Potential Role of the Rumen Microbiome in Milk Protein and Fat Synthesis in Dairy Cows Using Metagenomic Sequencing

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1247
Author(s):  
Xin Wu ◽  
Shuai Huang ◽  
Jinfeng Huang ◽  
Peng Peng ◽  
Yanan Liu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Amino Acid ◽  
Milk Fat ◽  
Milk Protein ◽  
Volatile Fatty Acids ◽  
Rumen Fluid ◽  
Abundant Species ◽  
Metagenomic Sequencing ◽  
Amino Acid Synthesis ◽  
Prevotella Species

The rumen contains abundant microorganisms that aid in the digestion of lignocellulosic feed and are associated with host phenotype traits. Cows with extremely high milk protein and fat percentages (HPF; n = 3) and low milk protein and fat percentages (LPF; n = 3) were selected from 4000 lactating Holstein cows under the same nutritional and management conditions. We found that the total concentration of volatile fatty acids, acetate, butyrate, and propionate in the rumen fluid was significantly higher in the HPF group than in the LPF group. Moreover, we identified 38 most abundant species displaying differential richness between the two groups, in which Prevotella accounted for 68.8% of the species, with the highest abundance in the HPF group. Functional annotation based on the Kyoto Encyclopedia of Gene and Genome (KEGG), evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG), and Carbohydrate-Active enzymes (CAZy) databases showed that the significantly more abundant species in the HPF group are enriched in carbohydrate, amino acid, pyruvate, insulin, and lipid metabolism and transportation. Furthermore, Spearman’s rank correlation analysis revealed that specific microbial taxa (mainly the Prevotella species and Neocallimastix californiae) are positively correlated with total volatile fatty acids (VFA). Collectively, we found that the HPF group was enriched with several Prevotella species related to the total VFA, acetate, and amino acid synthesis. Thereby, these fulfilled the host’s needs for energy, fat, and rumen microbial protein, which can be used for increased biosynthesis of milk fat and milk protein. Our findings provide novel information for elucidation of the regulatory mechanism of the rumen in the formation of milk composition.

scholarly journals Fecal microbiota dynamics during disease activity and remission in newly diagnosed and established ulcerative colitis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lena Öhman ◽  
Anders Lasson ◽  
Anna Strömbeck ◽  
Stefan Isaksson ◽  
Marcus Hesselmar ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Gut Microbiota ◽  
Disease Activity ◽  
Temporal Dynamics ◽  
Fecal Microbiota ◽  
Disease Stage ◽  
Dietary Interventions ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Specific Species

AbstractPatients with ulcerative colitis (UC) have an altered gut microbiota composition, but the microbial relationship to disease activity needs to be further elucidated. Therefore, temporal dynamics of the fecal microbial community during remission and flare was determined. Fecal samples were collected at 2–6 time-points from UC patients during established disease (cohort EST) and at diagnosis (cohort NEW). Sampling range for cohort EST was 3–10 months and for cohort NEW 36 months. Relapses were monitored for an additional three years for cohort EST. Microbial composition was assessed by Genetic Analysis GA-map Dysbiosis Test, targeting ≥ 300 bacteria. Eighteen patients in cohort EST (8 with maintained remission and 10 experiencing a flare), provided 71 fecal samples. In cohort NEW, 13 patients provided 49 fecal samples. The microbial composition showed no clustering related to disease activity in any cohort. Microbial dissimilarity was higher between than within patients for both cohorts, irrespective of presence of a flare. Microbial stability within patients was constant over time with no major shift in overall composition nor modification in the abundance of any specific species. Microbial composition was not affected by intensified medical treatment or linked to future disease course. Thus in UC, the gut microbiota is highly stable irrespective of disease stage, disease activity or treatment escalation. This suggests that prolonged dietary interventions or repeated fecal transplantations are needed to be able to induce permanent alterations of the gut microbiota.

scholarly journals Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Francesco Durazzi ◽  
Claudia Sala ◽  
Gastone Castellani ◽  
Gerardo Manfreda ◽  
Daniel Remondini ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Shotgun Sequencing ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Experimental Conditions ◽  
Rrna Gene Sequencing

AbstractIn this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

scholarly journals Green Tea and Its Relation to Human Gut Microbiome

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3907
Author(s):  
Sergio Pérez-Burillo ◽  
Beatriz Navajas-Porras ◽  
Alicia López-Maldonado ◽  
Daniel Hinojosa-Nogueira ◽  
Silvia Pastoriza ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Green Tea ◽  
Bacterial Species ◽  
Bioactive Molecules ◽  
Bioactive Metabolites ◽  
Microbial Dysbiosis ◽  
Inflammatory Processes ◽  
Health Promoting ◽  
Middle Man ◽  
Specific Species

Green tea can influence the gut microbiota by either stimulating the growth of specific species or by hindering the development of detrimental ones. At the same time, gut bacteria can metabolize green tea compounds and produce smaller bioactive molecules. Accordingly, green tea benefits could be due to beneficial bacteria or to microbial bioactive metabolites. Therefore, the gut microbiota is likely to act as middle man for, at least, some of the green tea benefits on health. Many health promoting effects of green tea seems to be related to the inter-relation between green tea and gut microbiota. Green tea has proven to be able to correct the microbial dysbiosis that appears during several conditions such as obesity or cancer. On the other hand, tea compounds influence the growth of bacterial species involved in inflammatory processes such as the release of LPS or the modulation of IL production; thus, influencing the development of different chronic diseases. There are many studies trying to link either green tea or green tea phenolic compounds to health benefits via gut microbiota. In this review, we tried to summarize the most recent research in the area.

scholarly journals Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

2017 ◽  
Vol 312 (4) ◽  
pp. G327-G339 ◽  
Author(s):  
Rebecca L. Knoll ◽  
Kristoffer Forslund ◽  
Jens Roat Kultima ◽  
Claudius U. Meyer ◽  
Ulrike Kullmer ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
Gut Microbiota ◽  
Bowel Disease ◽  
Virulence Genes ◽  
Metagenomic Sequencing ◽  
Fecal Microbiome ◽  
Microbial Dysbiosis ◽  
Healthy Siblings ◽  
Inflammatory Bowel ◽  
Sibling Study

Current treatment for pediatric inflammatory bowel disease (IBD) patients is often ineffective, with serious side effects. Manipulating the gut microbiota via fecal microbiota transplantation (FMT) is an emerging treatment approach but remains controversial. We aimed to assess the composition of the fecal microbiome through a comparison of pediatric IBD patients to their healthy siblings, evaluating risks and prospects for FMT in this setting. A case-control (sibling) study was conducted analyzing fecal samples of six children with Crohn’s disease (CD), six children with ulcerative colitis (UC) and 12 healthy siblings by metagenomic sequencing. In addition, lifetime antibiotic intake was retrospectively determined. Species richness and diversity were significantly reduced in UC patients compared with control [Mann-Whitney U-test false discovery rate (MWU FDR) = 0.011]. In UC, bacteria positively influencing gut homeostasis, e.g., Eubacterium rectale and Faecalibacterium prausnitzii, were significantly reduced in abundance (MWU FDR = 0.05). Known pathobionts like Escherichia coli were enriched in UC patients (MWU FDR = 0.084). Moreover, E. coli abundance correlated positively with that of several virulence genes (SCC > 0.65, FDR < 0.1). A shift toward antibiotic-resistant taxa in both IBD groups distinguished them from controls [MWU Benjamini-Hochberg-Yekutieli procedure (BY) FDR = 0.062 in UC, MWU BY FDR = 0.019 in CD). The collected results confirm a microbial dysbiosis in pediatric UC, and to a lesser extent in CD patients, replicating associations found previously using different methods. Taken together, these observations suggest microbiotal remodeling therapy from family donors, at least for children with UC, as a viable option. NEW & NOTEWORTHY In this sibling study, prior reports of microbial dysbiosis in IBD patients from 16S rRNA sequencing was verified using deep shotgun sequencing and augmented with insights into the abundance of bacterial virulence genes and bacterial antibiotic resistance determinants, seen against the background of data on the specific antibiotic intake of each of the study participants. The observed dysbiosis, which distinguishes patients from siblings, highlights such siblings as potential donors for microbiotal remodeling therapy in IBD.

scholarly journals Influence of dietary protein on Dahl salt-sensitive hypertension: a potential role for gut microbiota

2018 ◽  
Vol 315 (5) ◽  
pp. R907-R914 ◽  
Author(s):  
Justine M. Abais-Battad ◽  
David L. Mattson
Keyword(s):  
Gut Microbiota ◽  
Dietary Protein ◽  
Renal Damage ◽  
Potential Role ◽  
Dietary Interventions ◽  
Maternal Environment ◽  
Genetic And Environmental Factors ◽  
Salt Sensitive Hypertension ◽  
The Relationship ◽  
Insight Into

High blood pressure affects 1.39 billion adults across the globe and is the leading preventable cause of death worldwide. Hypertension is a multifaceted disease with known genetic and environmental factors contributing to its progression. Our studies utilizing the Dahl salt-sensitive (SS) rat have demonstrated the remarkable influence of dietary protein and maternal environment on the development of hypertension and renal damage in response to high salt. There is growing interest in the relationship between the microbiome and hypertension, with gut dysbiosis being correlated to a number of pathologies. This review summarizes the current literature regarding the interplay among dietary protein, the gut microbiota, and hypertension. These studies may provide insight into the effects we have observed between diet and hypertension in Dahl SS rats and, we hope, lead to new perspectives where potential dietary interventions or microbiota manipulations could serve as plausible therapies for hypertension.

scholarly journals Characteristics of Gut Microbiota in Children With Biliary Atresia After Liver Transplantation

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Song ◽  
Li-Ying Sun ◽  
Zhi-Jun Zhu ◽  
Lin Wei ◽  
Wei Qu ◽  
...  
Keyword(s):  
Liver Transplantation ◽  
Gut Microbiota ◽  
Biliary Atresia ◽  
Control Level ◽  
Control Group ◽  
Metagenomic Sequencing ◽  
Polyamine Biosynthesis ◽  
Fecal Samples ◽  
Linear Discriminant ◽  
Significant Difference

Background and AimsBiliary atresia (BA) is an idiopathic neonatal cholestasis and is the most common indication in pediatric liver transplantation (LT). Previous studies have suggested that the gut microbiota (GM) in BA is disordered. However, the effect of LT on gut dysbiosis in patients with BA has not yet been elucidated.MethodsPatients with BA (n = 16) and healthy controls (n = 10) were recruited. In the early life of children with BA, Kasai surgery is a typical procedure for restoring bile flow. According to whether BA patients had previously undergone Kasai surgery, we divided the post-LT patients into the with-Kasai group (n = 8) and non-Kasai group (n = 8). Fecal samples were collected in both the BA and the control group; among BA patients, samples were obtained again 6 months after LT. A total of 40 fecal samples were collected, of which 16 were pre-LT, 14 were post-LT (8 were with-Kasai, 6 were non-Kasai), and 10 were from the control group. Metagenomic sequencing was performed to evaluate the GM.ResultsThe Kruskal-Wallis test showed a statistically significant difference in the number of genes between the pre-LT and the control group, the pre-LT and the post-LT group (P &lt; 0.05), but no statistical difference between the post-LT and the control group. Principal coordinate analysis also showed that the microbiome structure was similar between the post-LT and control group (P &gt; 0.05). Analysis of the GM composition showed a significant decrease in Serratia, Enterobacter, Morganella, Skunalikevirus, and Phifllikevirus while short chain fatty acid (SCFA)-producing bacteria such as Roseburia, Blautia, Clostridium, Akkermansia, and Ruminococcus were increased after LT (linear discriminant analysis &gt; 2, P &lt; 0.05). However, they still did not reach the normal control level. Concerning functional profiles, lipopolysaccharide metabolism, multidrug resistance, polyamine biosynthesis, GABA biosynthesis, and EHEC/EPEC pathogenicity signature were more enriched in the post-LT group compared with the control group. Prior Kasai surgery had a specific influence on the postoperative GM.ConclusionLT partly improved the GM in patients with BA, which provided new insight into understanding the role of LT in BA.

scholarly journals Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus

2019 ◽  
Author(s):  
Feng Zhu ◽  
Yanmei Ju ◽  
Wei Wang ◽  
Qi Wang ◽  
Ruijin Guo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Validation Cohort ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Operating Characteristics ◽  
Discovery Cohort ◽  
Peripheral Tissues ◽  
Functional Changes ◽  
Microbial Biomarkers

AbstractEmerging evidence has linked the gut microbiota to schizophrenia. However, the functional changes in the gut microbiota and the biological role of individual bacterial species in schizophrenia have not been explored systematically. Here, we characterized the gut microbiota in schizophrenia using shotgun metagenomic sequencing of feces from a discovery cohort of 90 drug-free patients and 81 controls, as well as a validation cohort of 45 patients taking antipsychotics and 45 controls. We screened 83 schizophrenia-associated bacterial species and constructed a classifier comprising 26 microbial biomarkers that distinguished patients from controls with a 0.896 area under the receiver operating characteristics curve (AUC) in the discovery cohort and 0.765 AUC in the validation cohort. Our analysis of fecal metagenomes revealed that schizophrenia-associated gut–brain modules included short-chain fatty acids synthesis, tryptophan metabolism, and synthesis/degradation of neurotransmitters including glutamate, γ-aminobutyric acid, and nitric oxide. The schizophrenia-enriched gut bacterial species include several oral cavity-resident microbes, such as Streptococcus vestibularis. We transplanted Streptococcus vestibularis into the gut of the mice with antibiotic-induced microbiota depletion to explore its functional role. We observed that this microbe transiently inhabited the mouse gut and this was followed by hyperactivity and deficit in social behaviors, accompanied with altered neurotransmitter levels in peripheral tissues. In conclusion, our study identified 26 schizophrenia-associated bacterial species representing potential microbial targets for future treatment, as well as gut–brain modules, some of which may give rise to new microbial metabolites involved in the development of schizophrenia.

scholarly journals Immune Homeostasis: New Role of Micro- and Macroelements, Healthy Microbiota

2020 ◽  
Vol 6 (10) ◽  
pp. 206-233
Author(s):  
S. Bulgakova ◽  
N. Romanchuk
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Immune Responses ◽  
Immunological Tolerance ◽  
Immune Homeostasis ◽  
Individual Response ◽  
Protective Mechanisms ◽  
Medical Program ◽  
Genetic And Environmental Factors ◽  
The Individual

The availability of innovative technologies, such as next-generation sequencing and correlated bioinformatics tools, allows deeper investigation of the cross-network relationships between the microbiota and human immune responses. Immune homeostasis is the balance between immunological tolerance and inflammatory immune responses — a key feature in the outcome of health or disease. A healthy microbiota is the qualitative and quantitative ratio of diverse microbes of individual organs and systems, maintaining the biochemical, metabolic and immune equilibrium of the macroorganism necessary to preserve human health. The studies of P. I. Romanchuk found that the microbiota is a key element potentially capable of influencing antigen functions to induce a protective immune response and the ability of the immune system to adequately respond to antigenic stimulation (vaccine efficacy) by acting as an immunological modulator as well as a natural vaccine adjuvant. The mechanisms underlying the crosstalk between the gut microbiota and the immune system play a crucial role, especially at an early age (early gut microbiota forms immunological functions). New interactions, along with other genetic and environmental factors, lead to a certain composition and richness of the microbiota, which can diversify the individual response to vaccinations. Variations in microbial communities may explain the geographical effectiveness of vaccination. Modern technologies for quantifying the specific and functional characteristics of the microbiota of the gastrointestinal tract, along with fundamental and new concepts in the field of immunology, have revealed numerous ways in which the interaction of the host and microbiota proceeds favorably, neutrally or unfavorably. The gut microbiota has a strong influence on the shape and quality of the immune system, respectively, the immune system determines the composition and localization of the microbiota. Thus, a healthy microbiota directly modulates intestinal and systemic immune homeostasis. The new managed healthy biomicrobiota and personalized functional and balanced nutrition of the “brain and microbiota” is a patient's long-term medical program that allows the combined use of nutritional epigenetics and pharmacepigenetics, and most importantly, an increase in the protective mechanisms of immunity.

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