scholarly journals Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jason L. Anders ◽  
Mohamed Abdallah Mohamed Moustafa ◽  
Wessam Mohamed Ahmed Mohamed ◽  
Takashi Hayakawa ◽  
Ryo Nakao ◽  
...  
Keyword(s):  
Small Intestine ◽  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Host Species ◽  
Dietary Habits ◽  
Sympatric Species ◽  
Host Immune System ◽  
Wild Rodents ◽  
Apodemus Speciosus

AbstractHost–microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.

scholarly journals Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents

2021 ◽  
Author(s):  
Jason Anders ◽  
Alexis Mychajliw ◽  
Mohamed Moustafa ◽  
Wessam Mohamed ◽  
Takashi Hayakawa ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Urban Areas ◽  
Niche Breadth ◽  
Similar Species ◽  
Apodemus Speciosus ◽  
Dietary Shift ◽  
Animal Populations ◽  
Dietary Niche

Cities are among the most extreme forms of anthropogenic ecosystem modification and urbanization processes exert profound effects on animal populations through multiple ecological pathways. Increased access to human associated food items may alter species’ foraging behavior and diet, in turn modifying the normal microbial community of the gastrointestinal tract, ultimately impacting their health. It is crucial we understand the role of dietary niche breadth and the resulting shift in the gut microbiota as urban animals navigate novel dietary resources. We combined stable isotope analysis of hair and microbiome analysis of four gut regions across the gastrointestinal tract to investigate the effects of urbanization on the diet and gut microbiota of two sympatric species of rodent with different dietary niches; the omnivorous large Japanese field mouse (Apodemus speciosus) and the relatively more herbivorous grey red-backed vole (Myodes rufocanus). Both species exhibited an expanded dietary niche width within the urban areas potentially attributable to novel anthropogenic foods and altered resource availability. We detected a dietary shift in which urban A. speciosus consumed more terrestrial animal protein and M. rufocanus more plant leaves and stems. Such changes in resource use may be associated with an altered gut microbial community structure. There was an increased abundance of the presumably probiotic Lactobacillus in the small intestine of urban A. speciosus and potentially pathogenic Helicobacter in the colon of M. rufocanus. Together, these results suggest that even taxonomically similar species may exhibit divergent responses to urbanization with consequences for the gut microbiota and broader ecological interactions.

scholarly journals The Microbiotic Highway to Health—New Perspective on Food Structure, Gut Microbiota, and Host Inflammation

Nutrients ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1590 ◽  
Author(s):  
Nina Hansen ◽  
Anette Sams
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Dietary Habits ◽  
Gut Hormones ◽  
Host Immune System ◽  
Inflammatory Conditions ◽  
Food Structure ◽  
New Perspective ◽  
And Function ◽  
The Impact

This review provides evidence that not only the content of nutrients but indeed the structural organization of nutrients is a major determinant of human health. The gut microbiota provides nutrients for the host by digesting food structures otherwise indigestible by human enzymes, thereby simultaneously harvesting energy and delivering nutrients and metabolites for the nutritional and biological benefit of the host. Microbiota-derived nutrients, metabolites, and antigens promote the development and function of the host immune system both directly by activating cells of the adaptive and innate immune system and indirectly by sustaining release of monosaccharides, stimulating intestinal receptors and secreting gut hormones. Multiple indirect microbiota-dependent biological responses contribute to glucose homeostasis, which prevents hyperglycemia-induced inflammatory conditions. The composition and function of the gut microbiota vary between individuals and whereas dietary habits influence the gut microbiota, the gut microbiota influences both the nutritional and biological homeostasis of the host. A healthy gut microbiota requires the presence of beneficial microbiotic species as well as vital food structures to ensure appropriate feeding of the microbiota. This review focuses on the impact of plant-based food structures, the “fiber-encapsulated nutrient formulation”, and on the direct and indirect mechanisms by which the gut microbiota participate in host immune function.

scholarly journals Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa

2018 ◽  
Vol 115 (36) ◽  
pp. E8489-E8498 ◽  
Author(s):  
Pascale Vonaesch ◽  
Evan Morien ◽  
Lova Andrianonimiadana ◽  
Hugues Sanke ◽  
Jean-Robert Mbecko ◽  
...  
Keyword(s):  
Small Intestine ◽  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Bacterial Overgrowth ◽  
Oral Bacteria ◽  
Sub Saharan Africa ◽  
Growth Delay ◽  
Current View ◽  
Fecal Samples ◽  
Small Intestinal

Linear growth delay (stunting) affects roughly 155 million children under the age of 5 years worldwide. Treatment has been limited by a lack of understanding of the underlying pathophysiological mechanisms. Stunting is most likely associated with changes in the microbial community of the small intestine, a compartment vital for digestion and nutrient absorption. Efforts to better understand the pathophysiology have been hampered by difficulty of access to small intestinal fluids. Here, we describe the microbial community found in the upper gastrointestinal tract of stunted children aged 2–5 y living in sub-Saharan Africa. We studied 46 duodenal and 57 gastric samples from stunted children, as well as 404 fecal samples from stunted and nonstunted children living in Bangui, Central African Republic, and in Antananarivo, Madagascar, using 16S Illumina Amplicon sequencing and semiquantitative culture methods. The vast majority of the stunted children showed small intestinal bacterial overgrowth dominated by bacteria that normally reside in the oropharyngeal cavity. There was an overrepresentation of oral bacteria in fecal samples of stunted children, opening the way for developing noninvasive diagnostic markers. In addition, Escherichia coli/Shigella sp. and Campylobacter sp. were found to be more prevalent in stunted children, while Clostridia, well-known butyrate producers, were reduced. Our data suggest that stunting is associated with a microbiome “decompartmentalization” of the gastrointestinal tract characterized by an increased presence of oropharyngeal bacteria from the stomach to the colon, hence challenging the current view of stunting arising solely as a consequence of small intestine overstimulation through recurrent infections by enteric pathogens.

scholarly journals The Native Dietary Habits of the Two Sympatric Bee Species and Their Effects on Shaping Midgut Microorganisms

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Wang ◽  
Zhenfang Li ◽  
Lanting Ma ◽  
Guilin Li ◽  
Kai Han ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Growth And Development ◽  
Dietary Habits ◽  
Apis Cerana ◽  
Microbial Community Composition ◽  
Sympatric Species ◽  
Intestinal Microbial Community ◽  
Bee Bread ◽  
Before And After

The intestinal microbial community composition of different bee species typically has host specificity, yet little is known about the underlying formation mechanism. There are signs that dietary habits vary in different bee species, suggesting that there may be close relationships between dietary habits and intestinal microorganisms. We explored this hypothesis by comparing the dietary habits and gut microbiota of two common bee species (Apis mellifera L. and Apis cerana cerana) in China. Bee bread and midgut samples from wild and laboratory-reared bees were collected, and the differences in intestinal microbial community composition and growth and development before and after the change in dietary habits of different bee species were compared. We found that the two sympatric species had different dietary specializations and similar metagenomic diversities. The microbiota composition differed between the two species. Moreover, we revealed that changes in native dietary habits destroyed the intestinal microbiota community composition, negatively affecting the growth and development of honeybees.

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 Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

2018 ◽  
Author(s):  
Wei Yan ◽  
Jiangxia Zheng ◽  
Chaoliang Wen ◽  
Congliang Ji ◽  
Dexiang Zhang ◽  
...  
Keyword(s):  
Small Intestine ◽  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Fecal Samples ◽  
Community Membership ◽  
16S Rrna Amplicon Sequencing ◽  
Fecal Sampling

AbstractBackgroundDespite the convenience and noninvasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum and feces samples, for 16S rRNA amplicon sequencing analyses.ResultsIn this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11 – 87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54 – 0.71 and 0.71 – 0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the 4 gut segments, and these correlations were not high (ρ = −0.2 – 0.4, P < 0.05) for most genera.ConclusionsOur results provide evidence that the good potential of feces to identify most taxa in chicken guts, but it should be interpreted with caution by using feces as a proxy for gut in microbial structure analyses. This work provides insights and future directions regarding the usage of fecal samples in studies of the gut microbiome.

scholarly journals Understanding the interactions between Eimeria infection and gut microbiota, towards the control of chicken coccidiosis: a review

Parasite ◽  
2021 ◽  
Vol 28 ◽  
pp. 48
Author(s):  
Thabile Madlala ◽  
Moses Okpeku ◽  
Matthew Adekunle Adeleke
Keyword(s):  
Drug Resistance ◽  
Microbial Community ◽  
Gastrointestinal Tract ◽  
Gut Microbiota ◽  
Crucial Role ◽  
Parasite Infection ◽  
Alternative Strategies ◽  
Control And Prevention ◽  
Eimeria Infection ◽  
Diverse Microbial Community

The gastrointestinal tract in poultry harbours a diverse microbial community that serves a crucial role in digestion and protection. Disruption of the gut environment due to Eimeria spp. parasite infection causes an imbalance in intestinal homeostasis, driving the increment of pathogens such as Clostridium species. Coccidiosis infection affects the composition and integrity of gut microbiota, resulting in elevated susceptibility to diseases that pose a serious threat to the overall health and productivity of chickens. Anticoccidial drugs have proven effective in curbing coccidiosis but with concerning drawbacks like drug resistance and drug residues in meat. The exploration of natural alternative strategies such as probiotics and phytochemicals is significant in controlling coccidiosis through modification and restoration of gut microbiota, without inducing drug resistance. Understanding the interaction between Eimeria parasites and gut microbiota is crucial for the control and prevention of coccidiosis, and the development of novel alternative treatments.

Immunomodulatory Effect of “Dr. M.S. Reddy’s Multiple Mixed Strain Probiotic Therapy” to Cure or Prevent Hospital Acquired (Nosocomial) Infections due to Clostridium difficile (C. diff), other Pathogenic Bacteria, and Autoimmune Diseases

2018 ◽  
Vol 11 (1) ◽  
pp. 3937-3949
Author(s):  
Malireddy S Reddy
Keyword(s):  
Immune System ◽  
Gastrointestinal Tract ◽  
Pathogenic Bacteria ◽  
Molecular Level ◽  
Host Immune System ◽  
Hospital Acquired Infections ◽  
The World ◽  
Probiotic Strains ◽  
The Individual ◽  
Hospital Acquired

The worldwide popularity of Dr. M.S. Reddy’s Multiple Mixed Strain Probiotic Therapy to treat or prevent the hospital acquired infections (nosocomial infections) arose a great interest in the medical community around the world (Reddy and Reddy, 2016; 2017). The following questions were raised on this subject: Does Multiple Mixed Strain Probiotics directly inhibit the pathogenic bacteria (C. diff) in the gastrointestinal tract or indirectly through modulation of the host immune system or both? To be more specific, what is the exact and/or hypothetical mechanism at molecular level behind the breakthrough discovery of Dr. M.S. Reddy’s Multiple Mixed Strain Probiotic Therapy?  To answer these questions, the specific immunomodulation regulatory functions of the individual Probiotic strains (on host) have beenresearched, investigated andoutlined in this article.  A detailed explanation(s) and hypotheses have been proposed outlining the possible cumulativedirect bacteriological and indirect immunomodulatory effects (at the molecular level) of the Multiple Mixed Strain Probiotics used in Dr. M.S. Reddy’s Multiple Mixed Strain Probiotic Therapy to successfully treat C. diff infection.  A detailed scientific and research attempts were made to correlate the Probiotic induced immune activities in relation to the reduction of the symptoms associated with the hospital acquired Clostridium difficile infection during and after the Multiple Mixed Strain Probioitc Therapy.  Results of the clinical trials, microbiological tests on feces, and the clinical blood tests significantly revealed that the reasons for the success of Dr. Reddy’s Multiple Mixed Strain Probiotic Therapy are multifold. Presumably, it is predominantly due to the immunomodulatory effect they have exerted on the host immune system along with the direct inhibition of C. diff bacteria by multiple Probiotics, due to the production of bacteriocins, lactic acid and nutritional competency.In addition, the size of the individual cells of the Probiotic strains in the Multiple Mixed Strain Probiotics and their significant effect on immunomodulation has been thoroughly discussed. Results clearly proved that if Probiotics are absent in the GI tract during C. diff infection, the chances of patient survival is zero.  This is because of the excess immune stimulation and incurable damage to the epithelial cell barrier of the gastrointestinal tract caused by C. diff bacteria.  The results also revealed, without any doubt, as of to-datethe latest discovery of Dr. M.S. Reddy’s Multiple Mixed Strain Probiotic Therapy is the best way to cure the deadly hospital acquired infections affecting millions of people around the world, with high degree of mortality.  This has been attested by several practicng medical professionals and scientists around the world (Reddy and Reddy, 2017).

CHANGES IN SMALL INTESTINE MICROFLORA IN PATIENTS WITH ACUTE INTESTINAL OBSTRUCTION

2020 ◽  
pp. 16-18
Author(s):  
V. M. Lykhman ◽  
O. M. Shevchenko ◽  
Ye. O. Bilodid ◽  
Igor Vladimirovich Volchenko ◽  
I. A. Kulyk ◽  
...  
Keyword(s):  
Small Intestine ◽  
Gastrointestinal Tract ◽  
Species Composition ◽  
Intestinal Obstruction ◽  
Bacterial Flora ◽  
Anaerobic Bacteria ◽  
Acute Intestinal Obstruction ◽  
Gram Positive ◽  
Mechanical Intestinal Obstruction ◽  
Facultative Anaerobic Bacteria

Among urgent surgical diseases of abdominal cavity, an acute intestinal obstruction is the most difficult to be diagnosed and treated. Leading factor, determining the development of pathophysiological processes is considered to be the progressive manifestations of enteric insufficiency syndrome, resulting in intestinal barrier impairment, negative changes in ecology of intestinal flora, increased endotoxins. To identify the small intestine microflora in acute intestinal obstruction and determine the role of dysbiotic disorders in clinical manifestations of main pathological process, a study was conducted in 60 patients with mechanical intestinal obstruction. The small intestine has a relatively rare microflora, consisting mainly of gram−positive facultative aerobic microorganisms, streptococci, lactobacilli. The distal ileum in nearly 30−55 % of healthy people contains scanty microflora, and yet the flora of this area differs from the microbial population of the higher gastrointestinal tract due to higher concentration of gram−negative bacteria. Optional−anaerobic coliform bacilli, anaerobic bifidobacteria and fusobacteria, bacteroids, the number of which starts exceeding the one of gram−positive species, are presented in significant quantities. Distal to the ileocecal valve there are significant changes in the microflora quantitative and species composition. Obligatory anaerobic bacteria become the predominant part of microflora, exceeding the number of aerobic and facultative anaerobic bacteria. The bacterial flora in different parts of gastrointestinal tract has its own specifics and is quite constant, as a result of the interaction of many factors, regulating the bacterial population in small intestine. The most important among them are: acidity of gastric juice, normal peristaltic activity of the intestine, bacterial interactions and immune mechanisms. Disorders of the intestine motor and evacuation function with its obstruction lead to slow passage of the chyme and contamination of the upper gastrointestinal tract with new types of microbes. There is a syndrome of small intestine excessive colonization, which means an increased concentration of bacterial populations in it, similar in species composition to the colon microflora. Pathological intra−intestinal contents become a source of endogenous infection and re−infection of the patient, leads to internal digestive disorders, which is manifested by syndrome of malabsorption of proteins, carbohydrates and vitamins. Key words: acute intestinal obstruction, small intestinal microflora, conditionally pathogenic microorganisms, intestinal biocenosis.

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