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 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 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 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.

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.

scholarly journals The Studies to correlation between gut microbiota diversity and functional erectile dysfunction

2021 ◽  
Author(s):  
Qiang Geng ◽  
Shaofeng Chen ◽  
Yuan Sun ◽  
Yu Zhao ◽  
Zhong Li ◽  
...  
Keyword(s):  
Erectile Dysfunction ◽  
Gut Microbiota ◽  
Alpha Diversity ◽  
T Test ◽  
Data Quality Control ◽  
Sequencing Data ◽  
Significant Difference ◽  
Miseq Platform ◽  
Group 3 ◽  
Microbiota Diversity

Abstract Objective: To analyze the distribution of gut microbiota in the ED patients, and explore the relationship between the diversity of gut microbiota and psychogenic erectile dysfunction. Methods: 30 cases of patients with erectile dysfunction (ED) and 30 healthy persons (healthy donor, HD) stool specimen were collected, using Illumina's Miseq platform samples V3-V4 region sequences bacterial 16SrRNA gene Paired end (PE) 300 sequencing, sequencing results were analyzed differences in species composition and diversity. Analysis contains five modules: sequencing data quality control, OTU species clustering and annotation, alpha diversity, beta diversity and the use of T-test and the analysis of the LEfSe differences. Results: 1. The flora diversity in the group of ED than HD significantly different (P<0.01), ED group has a low bacterial diversity. 2. Between ED group and HD group, abundant bacteria (TOPlO) and core flora (90%) had no significant difference in the genus level; all bacteria flora (>1%) display, Alloprevotella groups genus presents differences, Alloprevotella only be identified in the HD group. 3. ED and HD groups present in well separated PCoA analysis, having a significant difference in the two kinds of microflora. 4.T-test shows six species were significantly different, in the ED group, Streptococcus and Subdoligranulum were increasing, and Prevotella, Prevotella sp.9, Blautia, Lachnospiraceae NK4A136 groups and Roseburia were decreasing. 5.LEfSe analysis revealed 24 species were significantly different between ED and HD groups. Conclusion: Gene sequencing was performed on the two groups of specimens and finding that microbial community structure and diversity had significant difference, suggesting that ED have low gut microbiota diversity.

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

scholarly journals High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yi-ran Chen ◽  
Hui-min Zheng ◽  
Guo-xia Zhang ◽  
Fang-lan Chen ◽  
Li-dan Chen ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Fasting Blood Glucose ◽  
Density Lipoprotein ◽  
Sleep Time ◽  
Host Health ◽  
Low Bmi ◽  
Gut Microbial Community ◽  
Fold Cross Validation

Abstract Oscillospira is a common yet rarely cultivated gut bacterial genus. Recently human gut microbiota studies have demonstrated its underlying significance for host health. However, little is known about Oscillospira-related host information and the links between Oscillospira and other members of the gut microbial community. To study the ecology of Oscillospira and gain insights into Oscillospira-related host physiological conditions, we analyzed data from the Guangdong Gut Microbiome Project, one of the largest gut microbiota database currently. Data of 6376 participants were analyzed. We studied the prevalence and relative abundance of Oscillospira as well as the profiles of associated microbial communities. We found that Oscillospira is closely related to human health because its abundance was positively correlated with microbial diversity, high density lipoprotein, and sleep time, and was inversely correlated with diastolic blood pressure, systolic blood pressure, fasting blood glucose, triglyceride, uric acid and Bristol stool type. Moreover, random forest analysis with five-fold cross validation showed Oscillospira could be a predictor of low BMI and constipation in the subset. Overall, in this study, we provide a basic understanding of Oscillospira-related microbiota profile and physiological parameters of the host. Our results indicate Oscillospira may play a role in aggravating constipation.

scholarly journals Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats

2020 ◽  
Vol 52 (7) ◽  
pp. 280-292 ◽  
Author(s):  
Katherine A. Maki ◽  
Larisa A. Burke ◽  
Michael W. Calik ◽  
Miki Watanabe-Chailland ◽  
Dagmar Sweeney ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Mean Arterial Pressure ◽  
Gut Microbiota ◽  
Arterial Pressure ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Sleep Fragmentation ◽  
Cardiovascular Pathology ◽  
Acid Producing Bacteria ◽  
Gut Microbial Community

The gut microbiota, via the production of metabolites entering the circulation, plays a role in blood pressure regulation. Blood pressure is also affected by the characteristics of sleep. To date, no studies have examined relationships among the gut microbiota/metabolites, blood pressure, and sleep. We hypothesized that fragmented sleep is associated with elevated mean arterial pressure, an altered and dysbiotic gut microbial community, and changes in fecal metabolites. In our model system, rats were randomized to 8 h of sleep fragmentation during the rest phase (light phase) or were undisturbed (controls) for 28 consecutive days. Rats underwent sleep and blood pressure recordings, and fecal samples were analyzed during: baseline ( days −4 to −1), early sleep fragmentation ( days 0–3), midsleep fragmentation ( days 6–13), late sleep fragmentation ( days 20–27), and recovery/rest ( days 28–34). Less sleep per hour during the sleep fragmentation period was associated with increased mean arterial pressure. Analyses of gut microbial communities and metabolites revealed that putative short chain fatty acid-producing bacteria were differentially abundant between control and intervention animals during mid-/late sleep fragmentation and recovery. Midsleep fragmentation was also characterized by lower alpha diversity, lower Firmicutes:Bacteroidetes ratio, and higher Proteobacteria in intervention rats. Elevated putative succinate-producing bacteria and acetate-producing bacteria were associated with lower and higher mean arterial pressure, respectively, and untargeted metabolomics analysis demonstrates that certain fecal metabolites are significantly correlated with blood pressure. These data reveal associations between sleep fragmentation, mean arterial pressure, and the gut microbiome/fecal metabolome and provide insight to links between disrupted sleep and cardiovascular pathology.

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