scholarly journals Mammalian gut metabolomes mirror microbiome composition and host phylogeny

2021 ◽  
Author(s):  
Rachel Gregor ◽  
Maraike Probst ◽  
Stav Eyal ◽  
Alexander Aksenov ◽  
Goor Sasson ◽  
...  
Keyword(s):  
Animal Species ◽  
Mammalian Species ◽  
Short Chain Fatty Acids ◽  
Taxonomic Composition ◽  
Mammalian Host ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Microbiome Composition ◽  
Host Phylogeny ◽  
Functionally Diverse

AbstractIn the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.

Modulation of instinal microbiom in the formation and progression of ulterative colitis.

2020 ◽  
Vol 75 (6) ◽  
pp. 577-584
Author(s):  
G. R. Bikbavova ◽  
M. A. Livzan
Keyword(s):  
Ulcerative Colitis ◽  
Short Chain Fatty Acids ◽  
Intestinal Wall ◽  
Intestinal Microbiome ◽  
Industrial Society ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Available Information ◽  
Post Industrial

In recent decades, an increase in the incidence of ulcerative colitis has been observed throughout the world. The purpose of this review is to generalize the available information on the influence of environmental factors and intestinal microbiome on the occurrence and development of ulcerative colitis, the role of bacteria metabolism products in the pathogenesis of the disease. Studied literature, we came to the conclusion that lifestyle in the era of post-industrial society has a significant impact on the microbial composition of the intestine and leads to changes in its diversity in patients suffering from ulcerative colitis. The changes include a decrease in the number of residential flora with anti-inflammatory activity, which synthesize short-chain fatty acids, and an increase in the number of potentially pathogenic and pathogenic microorganisms. Within the phylums Firmicutes and Proteobacteria, the proportional ratio changes. The combination of aggression factors (deterioration of the intestinal microbiome composition, the presence of aggressive intestinal metabolites) leads to intestinal mucosa permeability disfunction, impairing its barrier function. Food and bacterial agents can penetrate deeper layers of the intestinal wall through mucosal defects, which then stimulate the development of inflammatory and immune responses.

scholarly journals Shifts in microbiota species and fermentation products in a dietary model enriched in fat and sucrose

2015 ◽  
Vol 6 (1) ◽  
pp. 97-111 ◽  
Author(s):  
U. Etxeberria ◽  
N. Arias ◽  
N. Boqué ◽  
M.T. Macarulla ◽  
M.P. Portillo ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Intestinal Barrier ◽  
Short Chain Fatty Acids ◽  
Gas Chromatography Mass Spectrometry ◽  
Intestinal Barrier Function ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Inflammatory Status ◽  
Male Wistar Rats

The gastrointestinal tract harbours a ‘superorganism’ called the gut microbiota, which is known to play a crucial role in the onset and development of diverse diseases. This internal ecosystem, far from being a static environment, can be manipulated by diet and dietary components. Feeding animals with high-fat sucrose (HFS) diets entails diet-induced obesity, a model which is usually used in research to mimic the obese phenotype of Western societies. The aim of the present study was to identify gut microbiota dysbiosis and associated metabolic changes produced in male Wistar rats fed a HFS diet for 6 weeks and compare it with the basal microbial composition. For this purpose, DNA extracted from faeces at baseline and after treatment was analysed by amplification of the V4-V6 region of the 16S ribosomal DNA (rDNA) gene using 454 pyrosequencing. Short-chain fatty acids, i.e. acetate, propionate and butyrate, were also evaluated by gas chromatography-mass spectrometry. At the end of the treatment, gut microbiota composition significantly differed at phylum level (Firmicutes, Bacteroidetes and Proteobacteria) and class level (Erisypelotrichi, Deltaproteobacteria, Bacteroidia and Bacilli). Interestingly, the class Clostridia showed a significant decrease after HFS diet treatment, which correlated with visceral adipose tissue, and is likely mediated by dietary carbohydrates. Of particular interest, Clostridium cluster XIVa species were significantly reduced and changes were identified in the relative abundance of other specific bacterial species (Mitsuokella jalaludinii, Eubacterium ventriosum, Clostridium sp. FCB90-3, Prevotella nanceiensis, Clostridium fusiformis, Clostridium sp. BNL1100 and Eubacterium cylindroides) that, in some cases, showed opposite trends to their relative families. These results highlight the relevance of characterising gut microbial population differences at species level and contribute to understand the plausible link between diet and specific gut bacterial species that are able to influence the inflammatory status, intestinal barrier function and obesity development.

scholarly journals Daily feeding rhythm linked to microbiome composition in two zooplankton species

2021 ◽  
Author(s):  
Alaina C Pfenning-Butterworth ◽  
Reilly Cooper ◽  
Clay Cressler
Keyword(s):  
Feeding Behavior ◽  
Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Daily Feeding ◽  
Microbiome Diversity ◽  
Rrna Sequencing ◽  
Host Phylogeny ◽  
Induced Changes

Host-associated microbial communities are impacted by external and within-host factors, i.e., diet and feeding behavior. For organisms known to have a circadian rhythm in feeding behavior, microbiome composition is likely impacted by the different rates of microbe introduction and removal across a daily cycle, in addition to any diet-induced changes in microbial interactions. Here, we measured feeding behavior and used 16S rRNA sequencing to compare the microbial community across a diel cycle in two distantly related species of Daphnia, that differ in their life history traits, to assess how daily feeding patterns impact microbiome composition. We find that Daphnia species reared under similar laboratory conditions have significantly different microbial communities. Additionally, we reveal that Daphnia have daily differences in their microbial composition that correspond with feeding behavior, such that there is greater microbiome diversity at night during the host's active feeding phase. These results highlight that zooplankton microbiomes are relatively distinct and are likely influenced by host phylogeny.

scholarly journals The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2645
Author(s):  
Yelena Lapidot ◽  
Leah Reshef ◽  
Rebecca Goldsmith ◽  
Wasef Na’amnih ◽  
Eias Kassem ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Polyunsaturated Fatty Acids ◽  
Dietary Intake ◽  
Growth Period ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition

The intestinal microbiome continues to shift and develop throughout youth and could play a pivotal role in health and wellbeing throughout adulthood. Environmental and interpersonal determinants are strong mediators of the intestinal microbiome during the rapid growth period of preadolescence. We aim to delineate associations between the gut microbiome composition, body mass index (BMI), dietary intake and socioeconomic status (SES) in a cohort of ethnically homogenous preadolescents. This cohort included 139 Arab children aged 10–12 years, from varying socioeconomic strata. Dietary intake was assessed using the 24-h recall method. The intestinal microbiome was analyzed using 16S rRNA gene amplicon sequencing. Microbial composition was associated with SES, showing an overrepresentation of Prevotella and Eubacterium in children with lower SES. Higher BMI was associated with lower microbial diversity and altered taxonomic composition, including higher levels of Collinsella, especially among participants from lower SES. Intake of polyunsaturated fatty acids was the strongest predictor of bacterial alterations, including an independent association with Lachnobacterium and Lactobacillus. This study demonstrates that the intestinal microbiome in preadolescents is associated with socioeconomic determinants, BMI and dietary intake, specifically with higher consumption of polyunsaturated fatty acids. Thus, tailored interventions during these crucial years have the potential to improve health disparities throughout the lifespan.

The amount of rumen fluid influences the composition of short chain fatty acids produced in vitro

2006 ◽  
Vol 34 ◽  
pp. 87-92
Author(s):  
S. Muetzel ◽  
R.M. Mauricio ◽  
K. Becker
Keyword(s):  
Fatty Acids ◽  
Rumen Fluid ◽  
Short Chain Fatty Acids ◽  
Gas Production ◽  
Short Chain ◽  
Microbial Composition ◽  
Fatty Acid Production ◽  
Fermentation Products ◽  
Chain Fatty Acids

SummaryIn vitro rumen incubation systems are widely used to determine substrate degradation and the amount of fermentation products like gases, short chain fatty acids and the microbial biomass produced. Here we compare the influence of the amount of inoculum used for preparing the incubation medium on short chain fatty acid production and composition. Treatments were 10% and 30% (v/v) of filtered rumen fluid used for inoculation. In a series of experiments it was demonstrated that the two treatments did not alter the gas production or the amount of substrate truly degraded. However, SCFA production (especially acetate) was significantly reduced when only 10% of inoculum were used for incubation. We propose that acetate was taken up by rumen microorganisms as a precursor for growth, although it cannot be excluded that an altered microbial composition contributed to the observed differences.

Junction of the Epithelium and Lamina Propria of the Bovine Rumen Mucosa

1967 ◽  
Vol 25 ◽  
pp. 68-69
Author(s):  
Al W. Stinson
Keyword(s):  
Osmium Tetroxide ◽  
Squamous Epithelium ◽  
Short Chain Fatty Acids ◽  
Chloride Ions ◽  
Fermentation Products ◽  
Ruminant Species ◽  
Protective Shield ◽  
Stratified Squamous Epithelium ◽  
Lead Hydroxide ◽  
Acetic Acids

The stratified squamous epithelium which lines the ruminal compartment of the bovine stomach performs at least three important functions. (1) The upper keratinized layer forms a protective shield against the rough, fibrous, constantly moving ingesta. (2) It is an organ of absorption since a number of substances are absorbed directly through the epithelium. These include short chain fatty acids, potassium, sodium and chloride ions, water, and many others. (3) The cells of the deeper layers metabolize butyric acid and to a lesser extent propionic and acetic acids which are the fermentation products of rumen digestion. Because of the functional characteristics, this epithelium is important in the digestive process of ruminant species which convert large quantities of rough, fibrous feed into energy.Tissue used in this study was obtained by biopsy through a rumen fistula from clinically healthy, yearling holstein steers. The animals had been fed a typical diet of hay and grain and the ruminal papillae were fully developed. The tissue was immediately immersed in 1% osmium tetroxide buffered to a pH of 7.4 and fixed for 2 hrs. The tissue blocks were embedded in Vestapol-W, sectioned with a Porter-Blum microtome with glass knives and stained with lead hydroxide. The sections were studied with an RCA EMU 3F electron microscope.

Associations between gut microbiome, short chain fatty acids and blood pressure across ethnic groups: the HELIUS study

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
B Verhaar ◽  
D Collard ◽  
A Prodan ◽  
J.H.M Levels ◽  
A.H Zwinderman ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Fatty Acids ◽  
Ethnic Groups ◽  
Gut Microbiome ◽  
Short Chain Fatty Acids ◽  
Short Chain ◽  
Funding Source ◽  
Microbiome Composition ◽  
Helius Study ◽  
Chain Fatty Acids

Abstract Background Gut microbiome composition is shaped by a combination of host genetic make-up and dietary habits. In addition, large ethnic differences exist in microbiome composition. Several studies in humans and animals have shown that differences in gut microbiota and its metabolites, including short chain fatty acids (SCFA), are associated with blood pressure (BP). We hypothesized that gut microbiome composition and its metabolites may be differently associated with BP across ethnic groups. Purpose To investigate associations of gut microbiome composition and fecal SCFA levels with BP across different ethnic groups. Methods We assessed the association between gut microbiome composition and office BP among 4672 subjects (mean age 49.8±11.7 years, 52%F) of 6 different ethnic groups participating in the HELIUS study. Gut microbiome composition was determined using 16S rRNA sequencing. Associations between microbiome composition and blood pressure were assessed using machine learning prediction models. The resulting best predictors were correlated with BP using Spearman's rank correlations. Fecal SCFA levels were measured with high-performance liquid chromatography in an age- and body mass index (BMI)-matched subgroup of 200 participants with either extreme low or high systolic BP. Differences in abundances of best predictors and fecal SCFA levels between high and low BP groups were assessed with Mann-Whitney U tests. Results Gut microbiome composition explained 4.4% of systolic BP variance. Best predictors for systolic BP included Roseburia spp. (ρ −0.15, p<0.001), Clostridium spp. (ρ −0.14, p<0.001), Romboutsia spp. (ρ −0.10, p<0.001), and Ruminococceae spp. (ρ −0.15, p<0.001) (Figure 1). Explained variance of the microbiome composition was highest in Dutch subjects (4.8%), but very low in African Surinamese, Ghanaian, and Turkish ethnic groups (ranging from 0–0.77%) Hence, we selected only participants with Dutch ethnicity for the matched subgroup. Participants with high BP had lower abundance of Roseburia hominis (p<0.01) and Roseburia spp. (p<0.05) compared to participants with low BP. However, fecal acetate (p<0.05) and propionate (p<0.01) levels were higher in participants with high BP. Conclusions In this cross-sectional study, gut microbiome composition was moderately associated with BP. Associations were strongly divergent between ethnic groups, with strongest associations in Dutch participants. Intriguingly, while Dutch participants with high BP had lower abundances of several SCFA-producing microbes, they had higher fecal SCFA levels. Intervention studies with SCFAs could provide more insight in the effects of these metabolites on BP. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): The Academic Medical Center (AMC) of Amsterdam and the Public Health Service of Amsterdam (GGD Amsterdam) provided core financial support for HELIUS. The HELIUS study is also funded by research grants of the Dutch Heart Foundation (Hartstichting; grant no. 2010T084), the Netherlands Organization for Health Research and Development (ZonMw; grant no. 200500003), the European Integration Fund (EIF; grant no. 2013EIF013) and the European Union (Seventh Framework Programme, FP-7; grant no. 278901).

scholarly journals Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 726
Author(s):  
Ronald Biemann ◽  
Enrico Buß ◽  
Dirk Benndorf ◽  
Theresa Lehmann ◽  
Kay Schallert ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Weight Loss ◽  
Gut Microbiome ◽  
Taxonomic Composition ◽  
Low Grade ◽  
Gut Inflammation ◽  
Functional Changes ◽  
Microbiome Composition ◽  
Before And After ◽  
Human Proteins

Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (−13.7%), improved insulin sensitivity (HOMA-IR, −46.1%), and reduced levels of circulating hsCRP (−39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome.

scholarly journals Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 472
Author(s):  
Yeong-Ji Oh ◽  
Ye-Rin Park ◽  
Jungil Hong ◽  
Do-Yup Lee
Keyword(s):  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Metabolic Phenotype ◽  
Rrna Gene ◽  
Functional Evaluation ◽  
Initial Condition ◽  
Microbial Composition ◽  
Light Emitting ◽  
Blue Led ◽  
Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

scholarly journals Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Detman ◽  
Michał Bucha ◽  
Laura Treu ◽  
Aleksandra Chojnacka ◽  
Łukasz Pleśniak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Bacterial Species ◽  
Stable Carbon Isotope ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Core Microbiome ◽  
Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

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