scholarly journals The Regional Diversity of Gut Microbiome Along the GI Tract

2020 ◽  
Author(s):  
Enkhchimeg Lkhagv ◽  
Hea-Jong Chung ◽  
Jinny Hong ◽  
Wai Hong Wilson Tang ◽  
Sang-Il Lee ◽  
...  
Keyword(s):  
Research Work ◽  
Chemical Compositions ◽  
Gi Tract ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
Intestinal Microbes ◽  
Specific Manner ◽  
Microbiome Research ◽  
Metagenome Sequencing ◽  
Water Contents

Abstract Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location specific manner.Results: We first investigated the environmental conditions at 6 different locations along the along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different location of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific location and feces, we thoroughly analyzed the composition of microbiome of the GI contents and feces. Metagenome sequencing on the GI contents and feces showed presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE richness, Shannon diversity and Fisher’s alpha all indicated that the diversities of gut microbiota at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ilium while highest in cecum and colon. Interestingly, the diversities of fecal microbiome were lower than those of cecum and colon. Beta diversity analyses by NMDS plots, PCA, and un-supervised hierarchical clustering all showed that the microbiome compositions were very diverse in location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that fecal microbiome did not represent the microbiome of the whole GI tractConclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to the baseline assumption in the large majority of contemporary microbiome research work.

scholarly journals The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice

2020 ◽  
Author(s):  
Enkhchimeg Lkhagv ◽  
Hea-Jong Chung ◽  
Jinny Hong ◽  
Wai Hong Wilson Tang ◽  
Sang-Il Lee ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Research Work ◽  
Chemical Compositions ◽  
Gi Tract ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
Intestinal Microbes ◽  
Specific Manner ◽  
Metagenome Sequencing ◽  
Water Contents

Abstract Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of a human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location-specific manner.Results: We first investigated the environmental conditions at 6 different locations along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different locations of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific locations and feces, we thoroughly analyzed the composition of the microbiome of the GI contents and feces. 16S rDNA-based metagenome sequencing on the GI contents and feces showed the presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE (Abundance-based Coverage Estimator) richness, Shannon diversity, and Fisher’s alpha all indicated that the diversities of gut microbiome at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ileum while highest in cecum and colon. Interestingly, the diversities of the fecal microbiome were lower than those of the cecum and colon. Beta diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the microbiome compositions were very diverse in a location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that the fecal microbiome did not represent the microbiome of the whole GI tractConclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to a baseline assumption of contemporary microbiome research work.

scholarly journals The regional diversity of gut microbiome along the GI tract of male C57BL/6 mice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Enkhchimeg Lkhagva ◽  
Hea-Jong Chung ◽  
Jinny Hong ◽  
Wai Hong Wilson Tang ◽  
Sang-Il Lee ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Research Work ◽  
Chemical Compositions ◽  
Gi Tract ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
Intestinal Microbes ◽  
Specific Manner ◽  
Metagenome Sequencing ◽  
Water Contents

Abstract Background The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of a human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location-specific manner. Results We first investigated the environmental conditions at 6 different locations along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different locations of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific locations and feces, we thoroughly analyzed the composition of the microbiome of the GI contents and feces. 16S rDNA-based metagenome sequencing on the GI contents and feces showed the presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE (Abundance-based Coverage Estimator) richness, Shannon diversity, and Fisher’s alpha all indicated that the diversities of gut microbiome at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ileum while highest in cecum and colon. Interestingly, the diversities of the fecal microbiome were lower than those of the cecum and colon. Beta diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the microbiome compositions were very diverse in a location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that the fecal microbiome did not represent the microbiome of the whole GI tract. Conclusion The fecal microbiome is different from the whole microbiome of the GI tract, contrary to a baseline assumption of contemporary microbiome research work.

scholarly journals Positive Effect of Lactobacillus acidophilus EG004 on Cognitive Ability of Healthy Mice by Fecal Microbiome Analysis Using Full-Length 16S-23S rRNA Metagenome Sequencing

2022 ◽  
Author(s):  
Soomin Jeon ◽  
Hyaekang Kim ◽  
Jina Kim ◽  
Donghyeok Seol ◽  
Jinchul Jo ◽  
...  
Keyword(s):  
23S Rrna ◽  
Signal Molecules ◽  
Gi Tract ◽  
Signaling Mechanism ◽  
Fecal Microbiome ◽  
Microbiome Analysis ◽  
Short Period ◽  
Metagenome Sequencing ◽  
The Brain ◽  
Positive Effect

Recently, the concept of the “gut-brain axis” has risen and suggested that microbes in the GI tract affect the brain by modulating signal molecules. Although many pieces of research were reported in a short period, a signaling mechanism and the effects of a specific bacterial strain are still unclear.

scholarly journals A Petrologic and Noble Gas Isotopic Study of New Basaltic Eucrite Grove Mountains 13001 from Antarctica

Minerals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 279
Author(s):  
Chuantong Zhang ◽  
Bingkui Miao ◽  
Huaiyu He ◽  
Hongyi Chen ◽  
P. M. Ranjith ◽  
...  
Keyword(s):  
Noble Gas ◽  
Research Work ◽  
Cosmic Ray ◽  
Parent Body ◽  
Chemical Compositions ◽  
Isotopic Study ◽  
Impact Processes ◽  
Antarctic Research ◽  
Formation And Evolution ◽  
Grove Mountains

Howardite-Eucrite-Diogenite (HED) meteorite clan is a potential group of planetary materials which provides significant clues to understand the formation and evolution of the solar system. Grove Mountains (GRV) 13001 is a new member of HED meteorite, recovered from the Grove Mountains of Antarctica by the Chinese National Antarctic Research Expedition. This research work presents a comprehensive study of the petrology and mineralogy, chemical composition, noble gas isotopes, cosmic-ray exposure (CRE) age and nominal gas retention age for the meteorite GRV 13001. The output data indicate that GRV 13001 is a monomict basaltic eucrite with typical ophitic/subophitic texture, and it consists mainly of low-Ca pyroxene and plagioclase with normal eucritic chemical compositions. The noble gas based CRE age of the GRV 13001 is approximately 29.9 ± 3.0 Ma, which deviates from the major impact events or periods on the HED parent body. Additionally, the U,Th-4He and 40K-40Ar gas retention ages of this meteorite are ~2.5 to 4.0 Ga and ~3.6 to 4.1 Ga, respectively. Based on the noble gases isotopes and the corresponding ages, GRV 13001 may have experienced intense impact processes during brecciation, and weak thermal event after the ejection event at approximately 30 Ma.

scholarly journals Combined effect of mineralogical and chemical parameters on swelling behaviour of expansive soils

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bendadi Hanumantha Rao ◽  
Peddireddy Sreekanth Reddy ◽  
Bijayananda Mohanty ◽  
Krishna R. Reddy
Keyword(s):  
Expansive Soils ◽  
Research Work ◽  
Swelling Pressure ◽  
Combined Effect ◽  
Practical Significance ◽  
Chemical Compositions ◽  
Chemical Parameters ◽  
Swelling Behaviour ◽  
Mineral Contents ◽  
Swelling Properties

AbstractMicrolevel properties such as mineralogical and chemical compositions greatly control the macro behaviour of expansive soils. In this paper, the combined effect of mineral (i.e. montmorillonite, MMC) and chemical contents (i.e. Ca and Na in their total (T), leachable (L) and exchangeable form (CEC)) on swelling behaviour is investigated in a comprehensive way. Several 3-dimensional (3D) graphs correlating MMC and Ca/Na ratio, together, with swelling property (swelling potential, Sa, and swelling pressure, Sp) are developed. 3D plots, in general, portrayed a non-linear relationship of Sa and Sp with MMC and Ca/Na ratio, together. It is hypothesized that swelling initially is triggered by chemical parameters due to their quick and rapid ionization capability, but the overall swelling phenomenon is largely controlled by MMC. It is importantly found that expansive soils are dominant with divalent Ca++ ions up to MMC of 67% and beyond this percentage, monovalent Na+ ions are prevalent. From the interpretation of results, the maximum Sa of 18% and Sp of 93 kPa is measured at MMC of 43%, (Ca/Na)T of 10–14 and (Ca/Na)L of 2–7. It is concluded from study that total CEC + MMC for determining Sa and (Ca/Na)T + MMC for determining Sp are superior parameters to be considered. The findings of the study also excellently endorsed the results of Foster32, who stated that ionization of Na or Ca depends on the constituent mineral contents. The findings presented herein are unique, interesting and bear very practical significance, as no earlier research work reported such findings by accounting for chemical and mineralogical parameters impact, in tandem, on swelling properties.

CLAY-INORGANIC STUDIES. II. HYDROXY ALUMINUM PHOSPHATE–MONTMORILLONITE COMPLEX

1975 ◽  
Vol 55 (2) ◽  
pp. 225-233 ◽  
Author(s):  
H. KODAMA ◽  
M. D. WEBBER
Keyword(s):  
Relative Humidity ◽  
Room Temperature ◽  
Aluminum Phosphate ◽  
Silicate Layer ◽  
Basal Spacing ◽  
Minor Amount ◽  
Chemical Compositions ◽  
A Minor ◽  
Positively Charged ◽  
Water Contents

Two specimens of hydroxy aluminum phosphate interlayer materials in montmorillonite clay were prepared with 7.20 meq Al and 11.29 meq H3PO4/g clay and with 14.40 meq Al and 22.58 meq H3PO4/g clay, and the resulting complexes studied by chemical and mineralogical methods. Both interlayer materials were slightly positively charged and except for different water contents their chemical compositions were almost identical. They contained Al, PO4 and H2O and a minor amount of Ca and approximated hydrous AlPO4∙nH2O. The mole ratios of Al:Ca:PO4:OH were 1.00:0.08:0.92:0.24 and 1.00:0.05:0.91:0.24, respectively. The interlayer materials appeared to be loosely packed and distributed sparsely in interspaces of the montmorillonite. The degree of packing was greater for the preparation with the larger amount of interlayer material. The materials increased the montmorillonite basal spacing to 23.3 Å under air-dry condition (30–40% relative humidity) but did not affect the lateral dimensions. The basal spacing varied somewhat with relative humidity at room temperature and decreased markedly as water was driven off by heating. Heat treatments between room temperature and 300 C sharply reduced the d001 spacings to 16.7 Å which persisted up to 700 C. It is postulated that the large basal spacings occur because the hydrated interlayer materials have a framework structure with tunnels along the c-axis. This being so, changes in the spacings with different humidities might result from the movement of water molecules among interstitial spaces existing around and between the loosely distributed molecules of interlayer material. The 16.7 Å spacing for the dehydrated phase corresponds to the sum of 7.0 Å, the edge dimension of an orthorhombic anhydrous AlPO4 and 9.7 Å, the silicate layer thickness.

scholarly journals The effect of early social contact on the community structure and functions of  fecal microbiome in suckling - growing piglets

2020 ◽  
Author(s):  
Yanju Bi ◽  
Runze Liu ◽  
Wenbo Ji ◽  
Lei Pan ◽  
Haidong Wei ◽  
...  
Keyword(s):  
Social Environment ◽  
Intestinal Microbiota ◽  
Social Contact ◽  
Production Performance ◽  
Growth Stages ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
The Social ◽  
Negative Effect

Abstract Background: Social contact in the early suckling period as an enriched social environment can reduce the aggressive behaviors of piglets at weaning regrouping, and improve their production performance and welfare. We speculated that the social environment could modulate the maturation of piglet intestinal microbiota at later growth stages. Therefore, we performed microbial 16S rRNA gene sequencing from fecal samples, collected at 16, 35, 42, and 63 days of age, to investigate the structure and function of intestinal microbiota in piglets that experienced early social contact. Results: The results showed that the litter weight of the piglets was not significantly different between the control (CON) and social contact (SC) groups at 35 days of age (P > 0.05), but the weight of piglets in the SC group significantly decreased at 63 days compared to the CON group (P < 0.05). While the proportion of Firmicutes were the most abundant bacterial phylum detected in both groups at all times, the proportion of Firmicutes and the Firmicutes-to-Bacteroides ratio were significantly higher in the SC group compared to the CON group and the proportion of Bacteroides was lower in the SC group compared to the CON group at 35, 42, and 63 days of age (P < 0.05). At the genus level, early social contact had a significant positive effect on the level of Lactobacillus at 35 and 42 days of age (P < 0.05), but a negative effect on Prevotella at 35, 42, and 63 days of age (P < 0.05). Furthermore, functional analysis of the microbial composition showed that the changes induced by early social contact mainly altered the relative abundance of metabolic and related pathways. From 35 days of age, the social contact notably had a negative effect on the abundance microbial pathways for protein digestion and absorption and lipid metabolism (P < 0.05). Conclusions: Early social contact truly changed the taxonomy of fecal microbiota in piglets, which in turn, impacted the potential for microbial function within the piglet intestine. At present, we speculate that providing continuous social contact negatively influences the nutrient metabolism for the growing piglets.

scholarly journals The Impact of Environmental Chemicals on the Gut Microbiome

2020 ◽  
Vol 176 (2) ◽  
pp. 253-284 ◽  
Author(s):  
Karen Chiu ◽  
Genoa Warner ◽  
Romana A Nowak ◽  
Jodi A Flaws ◽  
Wenyan Mei
Keyword(s):  
Gut Microbiome ◽  
Current Knowledge ◽  
Environmental Chemicals ◽  
Microbial Composition ◽  
Multiple Factors ◽  
Microbiome Research ◽  
Health Related ◽  
Exogenous Factors ◽  
The Impact ◽  
Insight Into

Abstract Since the surge of microbiome research in the last decade, many studies have provided insight into the causes and consequences of changes in the gut microbiota. Among the multiple factors involved in regulating the microbiome, exogenous factors such as diet and environmental chemicals have been shown to alter the gut microbiome significantly. Although diet substantially contributes to changes in the gut microbiome, environmental chemicals are major contaminants in our food and are often overlooked. Herein, we summarize the current knowledge on major classes of environmental chemicals (bisphenols, phthalates, persistent organic pollutants, heavy metals, and pesticides) and their impact on the gut microbiome, which includes alterations in microbial composition, gene expression, function, and health effects in the host. We then discuss health-related implications of gut microbial changes, which include changes in metabolism, immunity, and neurological function.

scholarly journals Computational Modeling of the Human Microbiome

2020 ◽  
Vol 8 (2) ◽  
pp. 197
Author(s):  
Shomeek Chowdhury ◽  
Stephen S. Fong
Keyword(s):  
Computational Modeling ◽  
Human Health ◽  
Large Scale ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Microbial Composition ◽  
Site Specific ◽  
Microbiome Research ◽  
High Level ◽  
The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

scholarly journals Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Anna M. Seekatz ◽  
Matthew K. Schnizlein ◽  
Mark J. Koenigsknecht ◽  
Jason R. Baker ◽  
William L. Hasler ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Upper Gastrointestinal Tract ◽  
Rrna Gene ◽  
Gi Tract ◽  
Microbial Composition ◽  
Content Type ◽  
Healthy Humans ◽  
Health And Disease ◽  
Upper Gastrointestinal ◽  
Over Time

ABSTRACTAlthough the microbiota in the proximal gastrointestinal (GI) tract have been implicated in health and disease, much about these microbes remains understudied compared to those in the distal GI tract. This study characterized the microbiota across multiple proximal GI sites over time in healthy individuals. As part of a study of the pharmacokinetics of oral mesalamine administration, healthy, fasted volunteers (n = 8; 10 observation periods total) were orally intubated with a four-lumen catheter with multiple aspiration ports. Samples were taken from stomach, duodenal, and multiple jejunal sites, sampling hourly (≤7 h) to measure mesalamine (administered att = 0), pH, and 16S rRNA gene-based composition. We observed a predominance ofFirmicutesacross proximal GI sites, with significant variation compared to stool. The microbiota was more similar within individuals over time than between subjects, with the fecal microbiota being unique from that of the small intestine. The stomach and duodenal microbiota displayed highest intraindividual variability compared to jejunal sites, which were more stable across time. We observed significant correlations in the duodenal microbial composition with changes in pH; linear mixed models identified positive correlations with multipleStreptococcusoperational taxonomic units (OTUs) and negative correlations with multiplePrevotellaandPasteurellaceaeOTUs. Few OTUs correlated with mesalamine concentration. The stomach and duodenal microbiota exhibited greater compositional dynamics than the jejunum. Short-term fluctuations in the duodenal microbiota were correlated with pH. Given the unique characteristics and dynamics of the proximal GI tract microbiota, it is important to consider these local environments in health and disease states.IMPORTANCEThe gut microbiota are linked to a variety of gastrointestinal diseases, including inflammatory bowel disease. Despite this importance, microbiota dynamics in the upper gastrointestinal tract are understudied. Our article seeks to understand what factors impact microbiota dynamics in the healthy human upper gut. We found that the upper gastrointestinal tract contains consistently prevalent bacterial OTUs that dominate the overall community. Microbiota variability is highest in the stomach and duodenum and correlates with pH.

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