scholarly journals Introducing Murine Microbiome Database (MMDB): A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome

2019 ◽  
Vol 7 (11) ◽  
pp. 480 ◽  
Author(s):  
Yang ◽  
Park ◽  
Park ◽  
Baek ◽  
Chun
Keyword(s):  
Immune System ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Mouse Strains ◽  
The Internet ◽  
Rrna Gene ◽  
Healthy Mouse ◽  
Gastrointestinal Microbiome ◽  
Taxonomic Profiling ◽  
Biological Insight

The gut microbiota modulates overall metabolism, the immune system and brain development of the host. The majority of mammalian gut microbiota consists of bacteria. Among various model animals, the mouse has been most widely used in pre-clinical biological experiments. The significant compositional differences in taxonomic profiles among different mouse strains due to gastrointestinal locations, genotypes and vendors have been well documented. However, details of such variations are yet to be elucidated. This study compiled and analyzed 16S rRNA gene-based taxonomic profiles of 554 healthy mouse samples from 14 different projects to construct a comprehensive database of the microbiome of a healthy mouse gastrointestinal tract. The database, named Murine Microbiome Database, should provide researchers with useful taxonomic information and better biological insight about how each taxon, such as genus and species, is associated with locations in the gastrointestinal tract, genotypes and vendors. The database is freely accessible over the Internet at http://leb.snu.ac.kr/mmdb/.

Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

2019 ◽  
Author(s):  
Lara Parata ◽  
Shaun Nielsen ◽  
Xing Xing ◽  
Torsten Thomas ◽  
Suhelen Egan ◽  
...  
Keyword(s):  
Coral Reef ◽  
Gastrointestinal Tract ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Food Source ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Symbionts ◽  
Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

scholarly journals Geography as non-genetic modulation factor of chicken cecal microbiota

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244724
Author(s):  
Natalia Pin Viso ◽  
Enzo Redondo ◽  
Juan María Díaz Carrasco ◽  
Leandro Redondo ◽  
Julia Sabio y. Garcia ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Geographical Origin ◽  
Dominant Role ◽  
Geographical Location ◽  
Threshold Value ◽  
Production Performance ◽  
Rrna Gene ◽  
Cecal Microbiota ◽  
Chicken Gut Microbiota

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term “local microbiota” as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.

scholarly journals Levels of Main Bacterial Phyla in the Gastrointestinal Tract of Sheep Depending on Parity and Age

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2203
Author(s):  
Jakub Smoliński ◽  
Natalia Szeligowska ◽  
Paulina Cholewińska ◽  
Katarzyna Czyż ◽  
Marzena Janczak
Keyword(s):  
Immune System ◽  
Gastrointestinal Tract ◽  
Dna Isolation ◽  
The Body ◽  
Hormonal Changes ◽  
Gastrointestinal Microbiome ◽  
Bacterial Dna ◽  
Disease Symptoms ◽  
Bacterial Phyla ◽  
The Third

During pregnancy and parturition, the homeostasis of the body is disturbed, and the immune system is undermined, which is associated with hormonal changes within the body. Recently, it has also been suggested that physiological and hormonal changes associated with pregnancy may affect the composition of the gastrointestinal microbiome. Therefore, the aim of this study was to determine the composition of the microbiome in the third month of pregnancy in sheep in their first and second parity. Eighteen females in total were selected for the experiment, and they were divided into two groups: primiparous (aged 1 year) and multiparous ones (aged 2 years). The animals were fed the same fodder, and did not show any disease symptoms. Fecal samples were collected individually from each female (n = 20), and then bacterial DNA isolation and real-time PCR were performed for the main bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria) and families (Lactobacillaceae and Clostridia). The obtained results showed the differentiation in the microbiome between the primiparous and multiparous ewes with respect to the following groups: Bacteroidetes, Proteobacteria, and Actinobacteria—the level was higher in the case of the primiparas. These results suggest that the parity and age of the females may affect the gastrointestinal microbiome, but further studies are recommended.

scholarly journals Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18 and SARS-CoV-2-specific IgA

2020 ◽  
Author(s):  
Wanyin Tao ◽  
Shu Zhu ◽  
Guorong Zhang ◽  
Xiaofang Wang ◽  
Meng Guo ◽  
...  
Keyword(s):  
Immune System ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Disease Severity ◽  
Specific Cell ◽  
Host Immune System ◽  
Inflammatory Factor ◽  
Cytokine Storm

The current global COVID-19 pandemic is caused by beta coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which already infected over 10 million and caused 500 thousand deaths by June 2020. Overproduction of cytokines triggered by COVID-19 infection, known as "cytokine storm", is a highly risk factor associated with disease severity. However, how COVID-19 infection induce cytokine storm is still largely unknown. Accumulating in vitro and in vivo evidence suggests that gut is also susceptible to COVID19 infection: Human intestinal organoids, an in vitro model which mimic the specific cell type and spatial structure of the intestine, were susceptible to SARS-CoV2 infection; A significant fraction of patients reported gut symptoms; Viral RNA may persist for more than 30 days and infectious virus could be isolated in fecal samples. The gastrointestinal tract is the primary site of interaction between the host immune system with symbiotic and pathogenic microorganisms. The bacteria resident in our gastrointestinal tract, known as gut microbiota, is important to maintain the homeostasis of our immune system. While imbalance of gut microbiota, or dysbiosis, is associated with multiple inflammation diseases5. It's possible that SARS-CoV-2 infection may lead to alternation of gut microbiota thus worsen the host symptom. IL-18 is a proinflammatory cytokine produced multiple enteric cells, including intestinal epithelial cells (IECs), immune cells as well as enteric nervous system, and was shown to increase in the serum of COVID-19 patients. Immunoglobin A (IgA) is mainly produced in the mucosal surfaces, in humans 40-60mg kg-1 day-1 than all other immunoglobulin isotypes combined, and at least 80% of all plasma cells are located in the intestinal lamina propria. Recent study showed that SARS-CoV-2 specific IgA in the serum is positively correlate with the disease severity in COVID-19 patients11. Here we investigated the alterations of microbiota in COVID-19 patients, and its correlation with inflammatory factor IL-18 and SARS-CoV2 specific IgA.

scholarly journals Gut Microbiome, Probiotics and Bone: An Updated Mini Review

2019 ◽  
Vol 7 (3) ◽  
pp. 478-481
Author(s):  
Myriam Abboud ◽  
Dimitrios Papandreou
Keyword(s):  
Immune System ◽  
Gastrointestinal Tract ◽  
Bone Formation ◽  
Gut Microbiota ◽  
Direct Effect ◽  
Gut Microbiome ◽  
Endocrine System ◽  
Positive Effect

The gut microbiome is now considered as a large organ that has a direct effect on gastrointestinal tract, immune and endocrine system. There is no evidence that gut microbiota regulates the immune system and is responsible for bone formation and destruction. Probiotics have been shown through the gastrointestinal tract to have a positive effect on the management of the healthy bone. This article discusses the latest data available from PubMed and Scopus databases regarding gut microbiome, probiotics and bone briefly.

A Review and Roadmap of the Skin, Lung, and Gut Microbiota in Systemic Sclerosis

Rheumatology ◽  
2021 ◽  
Author(s):  
Shannon Teaw ◽  
Monique Hinchcliff ◽  
Michelle Cheng
Keyword(s):  
Experimental Study ◽  
Immune System ◽  
Systemic Sclerosis ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Microbial Species ◽  
Study Results ◽  
Environmental Trigger ◽  
The Relationship

Abstract As our understanding of the genetic underpinnings of systemic sclerosis (SSc) increases, questions regarding the environmental trigger(s) that induce and propagate SSc in the genetically predisposed individual emerge. The interplay between the environment, the immune system, and the microbial species that inhabit the patient’s skin and gastrointestinal tract is a pathobiological frontier that is largely unexplored in SSc. The purpose of this review is to provide an overview of the methodologies, experimental study results, and future roadmap for elucidating the relationship between the SSc host and his/her microbiome.

scholarly journals NEUROLOGICAL PERSPECTIVES OF GUT MICROBIOTA

2020 ◽  
Vol 4 (4) ◽  
Author(s):  
Bhupendra Chaudhary ◽  
Ansh Chaudhary
Keyword(s):  
Multiple Sclerosis ◽  
Type 2 Diabetes ◽  
Bipolar Disorder ◽  
Immune System ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Metabolic Diseases ◽  
Lipid Disorders ◽  
Anxiety Depression

The gut microbiota comprises of bacteria, viruses, protozoa and fungi living in different districts of human body with over 70% in gastrointestinal tract. They generally live in mutually beneficial relationships in gut. It has been proved that abnormalities in composition of microbiota are often associated with presence of common metabolic diseases, type 2 diabetes and lipid disorders. Recently gut microbiota are found to be major culprits in etiopathogenesis of various neuropsychiatric disorders which are triggered by stress induced down regulation of immune system of body. The association of gut microbiota with diseases like anxiety, depression, autism, bipolar disorder, Parkinson’s disease and multiple sclerosis has developed new insight in management of these diseases and advocates the need of further research in this area.

scholarly journals Partners in Infectious Disease: When Microbes Facilitate Enteric Viral Infections

2021 ◽  
Vol 12 (1) ◽  
pp. 41-55
Author(s):  
Kristen A. Engevik ◽  
Melinda A. Engevik
Keyword(s):  
Infectious Disease ◽  
Immune System ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Viral Infection ◽  
Viral Infections ◽  
Viral Fitness ◽  
Glycan Structure ◽  
Adhesion Sites ◽  
Diverse Community

The lumen of the gastrointestinal tract harbors a diverse community of microbes, fungi, archaea, and viruses. In addition to occupying the same enteric niche, recent evidence suggests that microbes and viruses can act synergistically and, in some cases, promote disease. In this review, we focus on the disease-promoting interactions of the gut microbiota and rotavirus, norovirus, poliovirus, reovirus, and astrovirus. Microbes and microbial compounds can directly interact with viruses, promote viral fitness, alter the glycan structure of viral adhesion sites, and influence the immune system, among other mechanisms. These interactions can directly and indirectly affect viral infection. By focusing on microbe–virus interplay, we hope to identify potential strategies for targeting offending microbes and minimizing viral infection.

scholarly journals Early-life gut dysbiosis linked to juvenile mortality in ostriches

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Elin Videvall ◽  
Se Jin Song ◽  
Hanna M. Bensch ◽  
Maria Strandh ◽  
Anel Engelbrecht ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Model Organisms ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Juvenile Mortality ◽  
Gut Dysbiosis ◽  
Stage Of Development ◽  
Fecal Sampling

Abstract Background Imbalances in the gut microbial community (dysbiosis) of vertebrates have been associated with several gastrointestinal and autoimmune diseases. However, it is unclear which taxa are associated with gut dysbiosis, and if particular gut regions or specific time periods during ontogeny are more susceptible. We also know very little of this process in non-model organisms, despite an increasing realization of the general importance of gut microbiota for health. Methods Here, we examine the changes that occur in the microbiome during dysbiosis in different parts of the gastrointestinal tract in a long-lived bird with high juvenile mortality, the ostrich (Struthio camelus). We evaluated the 16S rRNA gene composition of the ileum, cecum, and colon of 68 individuals that died of suspected enterocolitis during the first 3 months of life (diseased individuals), and of 50 healthy individuals that were euthanized as age-matched controls. We combined these data with longitudinal environmental and fecal sampling to identify potential sources of pathogenic bacteria and to unravel at which stage of development dysbiosis-associated bacteria emerge. Results Diseased individuals had drastically lower microbial alpha diversity and differed substantially in their microbial beta diversity from control individuals in all three regions of the gastrointestinal tract. The clear relationship between low diversity and disease was consistent across all ages in the ileum, but decreased with age in the cecum and colon. Several taxa were associated with mortality (Enterobacteriaceae, Peptostreptococcaceae, Porphyromonadaceae, Clostridium), while others were associated with health (Lachnospiraceae, Ruminococcaceae, Erysipelotrichaceae, Turicibacter, Roseburia). Environmental samples showed no evidence of dysbiosis-associated bacteria being present in either the food, water, or soil substrate. Instead, the repeated fecal sampling showed that pathobionts were already present shortly after hatching and proliferated in individuals with low microbial diversity, resulting in high mortality several weeks later. Conclusions Identifying the origins of pathobionts in neonates and the factors that subsequently influence the establishment of diverse gut microbiota may be key to understanding dysbiosis and host development.

scholarly journals Fighting Food Allergy by Inducing Oral Tolerance: Facts and Fiction

2021 ◽  
pp. 1-11
Author(s):  
Xiaotong Yang ◽  
Rui Liang ◽  
Qianlu Xing ◽  
Xiaojuan Ma
Keyword(s):  
Food Allergy ◽  
Immune System ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Food Processing ◽  
Oral Tolerance ◽  
Accidental Exposure ◽  
Related Factors ◽  
Processing Methods ◽  
Food Antigens

The prevalence of food allergy (FA) is increasing, and there is an urgent need to take effective measures against it. One important measure is the avoidance diet, which shows a disadvantage, especially in case of accidental exposure. Oral tolerance restoration sheds new light on the control of FA. Oral tolerance is naturally a state of systemic unresponsiveness of the gastrointestinal tract to food antigens and its restoration can be a clinical therapy for FA. Its immune basis lies on the intestinal mucosal immune system and factors, such as gut microbiota and food processing methods, are also important. This review presents recent advances in oral tolerance and its closely related factors.

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