scholarly journals gutMDisorder: a comprehensive database for dysbiosis of the gut microbiota in disorders and interventions

2019 ◽  
Vol 48 (D1) ◽  
pp. D554-D560 ◽  
Author(s):  
Liang Cheng ◽  
Changlu Qi ◽  
He Zhuang ◽  
Tongze Fu ◽  
Xue Zhang
Keyword(s):  
Gut Microbiota ◽  
Web Sites ◽  
Sequencing Data ◽  
Current Version ◽  
Gut Microbes ◽  
Beneficial Effects ◽  
Intervention Measures ◽  
User Friendly ◽  
Gut Microbial Community ◽  
Experimental Technology

Abstract gutMDisorder (http://bio-annotation.cn/gutMDisorder), a manually curated database, aims at providing a comprehensive resource of dysbiosis of the gut microbiota in disorders and interventions. Alterations in the composition of the gut microbial community play crucial roles in the development of chronic disorders. And the beneficial effects of drugs, foods and other intervention measures on disorders could be microbially mediated. The current version of gutMDisorder documents 2263 curated associations between 579 gut microbes and 123 disorders or 77 intervention measures in Human, and 930 curated associations between 273 gut microbes and 33 disorders or 151 intervention measures in Mouse. Each entry in the gutMDisorder contains detailed information on an association, including an intestinal microbe, a disorder name, intervention measures, experimental technology and platform, characteristic of samples, web sites for downloading the sequencing data, a brief description of the association, a literature reference, and so on. gutMDisorder provides a user-friendly interface to browse, retrieve each entry using gut microbes, disorders, and intervention measures. It also offers pages for downloading all the entries and submitting new experimentally validated associations.

scholarly journals gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites

2021 ◽  
Author(s):  
Liang Cheng ◽  
Changlu Qi ◽  
Haixiu Yang ◽  
Minke Lu ◽  
Yiting Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Target Genes ◽  
Metagenomic Sequencing ◽  
Microbial Metabolites ◽  
Gut Microbes ◽  
Intervention Measures ◽  
Mammalian Blood ◽  
Gut Microbe ◽  
User Friendly ◽  
The Relationship

Abstract gutMGene (http://bio-annotation.cn/gutmgene), a manually curated database, aims at providing a comprehensive resource of target genes of gut microbes and microbial metabolites in humans and mice. Metagenomic sequencing of fecal samples has identified 3.3 × 106 non-redundant microbial genes from up to 1500 different species. One of the contributions of gut microbiota to host biology is the circulating pool of bacterially derived small-molecule metabolites. It has been estimated that 10% of metabolites found in mammalian blood are derived from the gut microbiota, where they can produce systemic effects on the host through activating or inhibiting gene expression. The current version of gutMGene documents 1331 curated relationships between 332 gut microbes, 207 microbial metabolites and 223 genes in humans, and 2349 curated relationships between 209 gut microbes, 149 microbial metabolites and 544 genes in mice. Each entry in the gutMGene contains detailed information on a relationship between gut microbe, microbial metabolite and target gene, a brief description of the relationship, experiment technology and platform, literature reference and so on. gutMGene provides a user-friendly interface to browse and retrieve each entry using gut microbes, disorders and intervention measures. It also offers the option to download all the entries and submit new experimentally validated associations.

scholarly journals Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

2021 ◽  
Author(s):  
David Minich ◽  
Christopher Madden ◽  
Mauricio A. Navarro ◽  
Leo Glowacki ◽  
Kristen French-Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Treatment Plan ◽  
Type A ◽  
Toxin Gene ◽  
Sequencing Data ◽  
Intestinal Lesions ◽  
Rhodococcus Fascians ◽  
Human Care ◽  
Gut Microbial Community ◽  
Data Culture

AbstractBackgroundEnteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium – CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.ResultsWe employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis.ConclusionsWe identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

scholarly journals 3-(4-Hydroxy-3-methoxyphenyl)propionic Acid Produced from 4-Hydroxy-3-methoxycinnamic Acid by Gut Microbiota Improves Host Metabolic Condition in Diet-Induced Obese Mice

Nutrients ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 1036 ◽  
Author(s):  
Ryuji Ohue-Kitano ◽  
Satsuki Taira ◽  
Keita Watanabe ◽  
Yuki Masujima ◽  
Toru Kuboshima ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
Gut Microbiota ◽  
Propionic Acid ◽  
Fruits And Vegetables ◽  
Hepatic Lipid Metabolism ◽  
Beneficial Effects ◽  
Coffee Beans ◽  
Methoxycinnamic Acid ◽  
Gut Microbial Community ◽  
Hydroxycinnamic Acid Derivative

4-Hydroxy-3-methoxycinnamic acid (HMCA), a hydroxycinnamic acid derivative, is abundant in fruits and vegetables, including oranges, carrots, rice bran, and coffee beans. Several beneficial effects of HMCA have been reported, including improvement of metabolic abnormalities in animal models and human studies. However, its mitigating effects on high-fat diet (HFD)-induced obesity, and the mechanism underlying these effects, remain to be elucidated. In this study, we demonstrated that dietary HMCA was efficacious against HFD-induced weight gain and hepatic steatosis, and that it improved insulin sensitivity. These metabolic benefits of HMCA were ascribable to 3-(4-hydroxy-3-methoxyphenyl)propionic acid (HMPA) produced by gut microbiota. Moreover, conversion of HMCA into HMPA was attributable to a wide variety of microbes belonging to the phylum Bacteroidetes. We further showed that HMPA modulated gut microbes associated with host metabolic homeostasis by increasing the abundance of organisms belonging to the phylum Bacteroidetes and reducing the abundance of the phylum Firmicutes. Collectively, these results suggest that HMPA derived from HMCA is metabolically beneficial, and regulates hepatic lipid metabolism, insulin sensitivity, and the gut microbial community. Our results provide insights for the development of functional foods and preventive medicines, based on the microbiota of the intestinal environment, for the prevention of metabolic disorders.

scholarly journals Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

2022 ◽  
Vol 4 (1) ◽  
Author(s):  
David Minich ◽  
Christopher Madden ◽  
Mauricio A. Navarro ◽  
Leo Glowacki ◽  
Kristen French-Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Treatment Plan ◽  
Type A ◽  
Toxin Gene ◽  
Sequencing Data ◽  
Intestinal Lesions ◽  
Rhodococcus Fascians ◽  
Human Care ◽  
Gut Microbial Community ◽  
Data Culture

Abstract Background Enteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium—CZA; Denver Zoo—DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility. Results We employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis. Conclusions We identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

scholarly journals Dynamic Colonization of Gut Microbiota and Its Influencing Factors Among The Breast-Feeding Infants During The First Two Year of Life

2021 ◽  
Author(s):  
Ping Li ◽  
Xuelian Chang ◽  
Xiaoyu Chen ◽  
Tiantian Tang ◽  
Yajing Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Growth And Development ◽  
First Year ◽  
Sequencing Data ◽  
Normal Range ◽  
Healthy Mother ◽  
Rrna Sequencing ◽  
First Year Of Life ◽  
Gut Microbial Community

Abstract Background Maturation of the infant gut microbiota has lifelong implications on health, which has been proposed as the major events during the first year of life. However, little was known about dynamic colonization of the gut microbiota and its influencing elements among the two-year infancy as well as into the adulthood. Results Based on the 16S rRNA sequencing data in the V3-V4 regions among 30 healthy mother-infant pairs with the normal range of the growth and development index from birth to two years old, the diversity of the gut microbiota was significantly increased from Six-month to Two-year subgroups. Furthermore, the dynamic colonization of gut microbiota was that the significant trends of Firmicutes (Faecalibacterium, Blautia, Enterococcus, Subdoligranulum, Agathobacter, Unidentified_Erysipelotrichaceae, Staphylococcus, Acinetobacillus, Unidentified_ Ruminococcaceae and Fusicatenibacter), Bacteroidetes and Verrucomicrobia were increased, while Actinobacteria (Bifidobacterium) and Proteobacteria (Enterobacteriaceae and Klebsiella) were decreased with the increased age at the phylum and genus levels. These above results revealed that certain bacteria might modulate the host pathways, such as Chemoheterotrophy, Fermentation, Parasites_or _symbionts, Nitrate_reduction and Aerobic_chemoheterotrophy metabolism. Moreover, there were significant associations between maternal (gut microbiota in the milk, Pre-pregnancy BMI-M.BMI, BMI gain during the pregnancy-I.BMI) and infant characteristics (BMI at birth-B.BMI and increment of BMI-G.BMI), and the compositions of gut microbiota in the faeces, but not differences were shown between the different sex and mode of productive subgroups. Conclusion Overall, the gut microbial community was significantly matured into adulthood with the increased age subgroups. It also identified that there were significant correlations between the features of gut microbiota and maternal (gut microbiota in the milk, M.BMI and I.BMI) and infant characteristics (B.BMI and G.BMI), which will provide a new direction for the host-gut microbiota interplay during the two years of life.

scholarly journals Community-Wide Response of the Gut Microbiota to Enteropathogenic Citrobacter rodentium Infection Revealed by Deep Sequencing

2009 ◽  
Vol 77 (10) ◽  
pp. 4668-4678 ◽  
Author(s):  
Christian Hoffmann ◽  
David A. Hill ◽  
Nana Minkah ◽  
Thomas Kirn ◽  
Amy Troy ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Deep Sequencing ◽  
Distal Colon ◽  
Proximal Colon ◽  
Rrna Gene ◽  
Citrobacter Rodentium ◽  
Sequencing Data ◽  
Adaptive Immune ◽  
Gut Microbial Community

ABSTRACT We investigated the spatial and temporal response of the murine gut microbiome to infection with Citrobacter rodentium, an attaching-and-effacing bacterium that provokes innate and adaptive immune responses, resulting in transient bacterial colitis. Previous studies have suggested that C. rodentium-induced inflammation is associated with an increased abundance of Enterobacteriaceae. We report here a deeper analysis of this model using DNA bar coding and 454 pyrosequencing to characterize 101,894 partial 16S rRNA gene sequences from 85 microbial samples from tissue-adhered and luminal bacteria of the cecum, proximal colon, and distal colon, which allowed us to identify previously unappreciated spatial and kinetic changes in multiple bacterial lineages. The deep sequencing data revealed that C. rodentium was most abundantly associated with the cecal mucosa at day 9 postinfection and then diminished in abundance, providing the first reported use of deep sequencing to track a pathogen in vivo through the course of infection. Notable changes were associated with both the mucosally adhered and luminal microbiota at both day 9 and day 14 postinfection. Alterations in abundance were seen for Proteobacteria, Deferribacteres, Clostridia, and others; however, changes in Enterobacteriaceae could be accounted for by the presence of C. rodentium itself, which is a member of this family. The Lactobacillus group decreased in abundance during infection, which may be important for pathogenesis because members of this lineage modulate the composition of the gut microbiota and are used as probiotics. Thus, deep sequencing provides previously inaccessible information on how Citrobacter infection and clearance reshapes the gut microbial community in space and time.

Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy

2020 ◽  
Vol 17 (4) ◽  
pp. 498-506 ◽  
Author(s):  
Pavan K. Mujawdiya ◽  
Suman Kapur
Keyword(s):  
Microbial Community ◽  
Quorum Sensing ◽  
Population Density ◽  
Gut Microbiota ◽  
Biofilm Formation ◽  
Chemical Interaction ◽  
Bacterial Species ◽  
Critical Role ◽  
Bacterial Cells ◽  
Gut Microbes

: Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as “auto-inducers”. The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. : The human gut is home to trillions of bacterial cells collectively called “gut microbiota” or “gut microbes”. Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as “the forgotten organ” by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. : Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

scholarly journals PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes

2021 ◽  
Vol 22 (6) ◽  
pp. 3077
Author(s):  
Zhenzhen Hao ◽  
Xiaolu Wang ◽  
Haomeng Yang ◽  
Tao Tu ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Cell Wall ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Cell Wall Polysaccharide ◽  
Prominent Feature ◽  
Cell Wall Polysaccharides ◽  
Gut Microbial Community

Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.

Study on supplementary food with beneficial effects on the gut microbiota of infants

2021 ◽  
pp. 101291
Author(s):  
Shengnan Liang ◽  
Qinggang Xie ◽  
Smith Etareri Evivie ◽  
Lina Zhao ◽  
Qingxue Chen ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Supplementary Food ◽  
Beneficial Effects
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