scholarly journals Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Louise B. Thingholm ◽  
Corinna Bang ◽  
Malte C. Rühlemann ◽  
Annika Starke ◽  
Florian Sicks ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Homo Sapiens ◽  
Inflammatory Diseases ◽  
General Pattern ◽  
Amplicon Sequencing ◽  
Controlled Study ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Host Phylogeny

AbstractCompared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 368 stool samples from 38 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans.By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in westernized humans and platyrrhines, which is probably not only due to diet, but also to the social behavior and structure in these communities.Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammalian fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in westernized communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes, which promote the etiology of chronic diseases.

scholarly journals Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans

2021 ◽  
Author(s):  
Louise B. Thingholm ◽  
Corinna Bang ◽  
Malte C. Rühlemann ◽  
Annika Starke ◽  
Florian Sicks ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Homo Sapiens ◽  
Inflammatory Diseases ◽  
General Pattern ◽  
Controlled Study ◽  
Rrna Gene ◽  
New World Monkeys ◽  
Microbiota Composition ◽  
Host Phylogeny

Abstract Background: Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 424 stool samples from 40 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans.Results: By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in urban humans and New World monkeys, which is probably not only due to diet, but also to the social behavior of these communities.Conclusion: Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammals’ fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in urban communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes promoting the etiology of chronic diseases.

scholarly journals Ecology Impacts The Decrease of Spirochaetes and Prevotella In The Fecal Gut Microbiota of Urban Humans

2021 ◽  
Author(s):  
Louise B. Thingholm ◽  
Corinna Bang ◽  
Malte C. Rühlemann ◽  
Annika Starke ◽  
Florian Sicks ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Homo Sapiens ◽  
Inflammatory Diseases ◽  
General Pattern ◽  
Controlled Study ◽  
Rrna Gene ◽  
New World Monkeys ◽  
Microbiota Composition ◽  
Host Phylogeny

Abstract Background: Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 424 stool samples from 40 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans.Results: By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in urban humans and New World monkeys, which is probably not only due to diet, but also to the social behavior of these communities.Conclusion: Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammals’ fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in urban communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes promoting the etiology of chronic diseases.

scholarly journals Comparative Analysis of Fecal Microbiota Composition Between Rheumatoid Arthritis and Osteoarthritis Patients

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 748 ◽  
Author(s):  
Jin-Young Lee ◽  
Mohamed Mannaa ◽  
Yunkyung Kim ◽  
Jehun Kim ◽  
Geun-Tae Kim ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Stool Samples ◽  
Gut Microbiota Composition

The aim of this study was to investigate differences between the gut microbiota composition in patients with rheumatoid arthritis (RA) and those with osteoarthritis (OA). Stool samples from nine RA patients and nine OA patients were collected, and DNA was extracted. The gut microbiome was assessed using 16S rRNA gene amplicon sequencing. The structures and differences in the gut microbiome between RA and OA were analyzed. The analysis of diversity revealed no differences in the complexity of samples. The RA group had a lower Bacteroidetes: Firmicutes ratio than did the OA group. Lactobacilli and Prevotella, particularly Prevotella copri, were more abundant in the RA than in the OA group, although these differences were not statistically significant. The relative abundance of Bacteroides and Bifidobacterium was lower in the RA group. At the species level, the abundance of certain bacterial species was significantly lower in the RA group, such as Fusicatenibacter saccharivorans, Dialister invisus, Clostridium leptum, Ruthenibacterium lactatiformans, Anaerotruncus colihominis, Bacteroides faecichinchillae, Harryflintia acetispora, Bacteroides acidifaciens, and Christensenella minuta. The microbial properties of the gut differed between RA and OA patients, and the RA dysbiosis revealed results similar to those of other autoimmune diseases, suggesting that a specific gut microbiota pattern is related to autoimmunity.

scholarly journals Sex-dependent Gut Microbiota-brain-cognition Associations: A Multimodal MRI Study

2020 ◽  
Author(s):  
Shujun Zhang ◽  
Huanhuan Cai ◽  
Chunli Wang ◽  
Cun Zhang ◽  
Wenming Zhao ◽  
...  
Keyword(s):  
White Matter ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Behavioral Inhibition ◽  
Gray Matter Volume ◽  
Amplicon Sequencing ◽  
Influential Factor ◽  
Rrna Gene ◽  
The Right ◽  
The Brain

Abstract Background: There is bidirectional communication between the gut microbiota and the brain. Empirical evidence has demonstrated sex differences in both the gut microbiome and the brain. However, the effects of sex on the gut microbiota-brain associations have yet to be determined. Methods: 157 healthy young adults underwent brain structural, perfusion, functional and diffusion MRIs to measure gray matter volume (GMV), cerebral blood flow (CBF), functional connectivity strength (FCS) and white matter integrity, respectively. Fecal samples were collected and 16S rRNA gene amplicon sequencing was utilized to assess gut microbial diversity. Correlation analyses were conducted to test for sex-dependent associations between microbial diversity and brain imaging parameters, and mediation analysis was performed to further characterize the gut microbiota-brain-cognition relationship. Results: We found that higher gut microbial diversity was associated with higher GMV in the right cerebellum Ⅵ, higher CBF in the bilateral calcarine sulcus yet lower CBF in the left superior frontal gyrus, higher FCS in the bilateral paracentral lobule, and lower diffusivity in widespread white matter regions in males. However, these associations were absent in females. Of more importance, these neuroimaging biomarkers significantly mediated the association between gut microbial diversity and behavioral inhibition in males. Conclusions: These findings highlight sex as a potential influential factor underlying the gut microbiota-brain-cognition relationship, and expose the gut microbiota as a biomarker-driven and sex-sensitive intervention target for mental disorders with abnormal behavioral inhibition.

scholarly journals Exploring the resident gut microbiota of stranded odontocetes: high similarities between two dolphin species Tursiops truncatus and Stenella coeruleoalba

2020 ◽  
Vol 100 (7) ◽  
pp. 1181-1188
Author(s):  
Khaled F. A. Abdelrhman ◽  
Alice Ciofini ◽  
Giovanni Bacci ◽  
Cecilia Mancusi ◽  
Alessio Mengoni ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Tursiops Truncatus ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Cetacean Species ◽  
Stenella Coeruleoalba ◽  
Interspecific Differences ◽  
Gut Microbiota Composition

AbstractThe evaluation of symbiotic microbial communities occurring in the intestinal tract of animals has received great interest in recent years. However, little is known about gut microbial communities in cetaceans, despite their relevance in the ecology of marine communities. Here, we report an investigation using 16S rRNA gene amplicon sequencing of the resident gut microbiota of the two cetacean species Stenella coeruleoalba and Tursiops truncatus by sampling intestinal mucosa from specimens retrieved stranded along the Tyrrhenian coast of Tuscany (Italy). We found an abundance of members from Clostridiaceae and Fusobacteriaceae, which in total accounted for more than 50% of reads, in agreement with gut microbiota composition of other carnivorous mammals. Probably due to the limited number of samples available, sex, preservation status and also species, did not correlate with overall differences in the microbiota. Indeed, a high similarity of the taxonomic (family-level) composition between the gut microbiota of the two species was found. However, Pedobacter spp. was found abundant in amplicon sequencing libraries from S. coeruleoalba, while clostridia were more abundant from T. truncatus samples. Our results shed some light on the gut microbiota composition of two dolphin (S. coeruleoalba and T. truncatus) species, with specimens collected in the wild. Studies with a larger number of individuals are now needed to confirm these first results and evaluate the interspecific differences in relation to sex and age.

scholarly journals Caecal Microbiota Composition of Experimental Laying Hens Differs According to Genetic Line and Vaccination to IBV

2021 ◽  
Author(s):  
Marion Borey ◽  
Bertrand Bed'Hom ◽  
Nicolas Bruneau ◽  
Jordi Estellé ◽  
Frederik Larsen ◽  
...  
Keyword(s):  
T Cells ◽  
Gut Microbiota ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Genetic Line ◽  
Vaccine Response ◽  
Main Components ◽  
Main Association ◽  
Caecal Microbiota

Abstract BackgroundInteractions between the gut microbiota and the immune system may be involved in the vaccine response. In the present study, we studied the correlations between caecal microbiota composition and the immune response in six experimental laying hen lines harboring different haplotypes at the Major Histocompatibility complex (MHC), 7 weeks after their first vaccination against the infectious bronchitis virus (IBV). Two lines were previously considered as high responders (HR) to IBV vaccination and two other ones as low responders (LR). We explored to what extent the gut microbiota could be related to this variability through the characterization of caecal bacterial communities with a 16S rRNA gene amplicon sequencing approach, one week after an IBV infectious challenge. ResultsWe observed significant effects of both the vaccination and the genetic line on the microbiota, with lower bacterial richness in vaccinated chickens, especially in the Ruminococcaceae family. We also observed dissimilar caecal communities among the different MHC lines, and among the vaccinated and non-vaccinated animals. The effect of vaccination was similar in all the lines, with a reduced abundance of OTUs from the Ruminococcacea UCG-014 and Faecalibacterium genera, and an increased abundance of OTUs from the Eisenbergiella genus. The main association between the microbiota and the immune phenotypes implied TCRϒδ expression on TCRϒδ+ T cells, which especially shared negative associations with OTUs from the Escherichia-Shigella genus. Finally, opposing the HR and LR groups, we identified 3 OTUs more abundant in the HR group, from the Tyzzeralla family, the Angelakisella genus, and to a lower extent the Flavonifractor family. Conversely, an OTU from the CAG-352 genus was more abundant in the LR group. ConclusionsWe assessed that the caecal microbiota composition is associated with the IBV vaccine response in laying chickens, and that TCRϒδ expression on TCRϒδ+ T cells appears as one of the main components potentially involved in this interaction.

scholarly journals Changes in human gut microbiota composition are linked to the energy metabolic switch during 10 d of Buchinger fasting

2019 ◽  
Vol 8 ◽  
Author(s):  
Robin Mesnage ◽  
Franziska Grundler ◽  
Andreas Schwiertz ◽  
Yvon Le Maho ◽  
Françoise Wilhelmi de Toledo
Keyword(s):  
Gut Microbiota ◽  
Inflammatory Diseases ◽  
Well Being ◽  
Amplicon Sequencing ◽  
Serum Biochemistry ◽  
Rrna Gene ◽  
Human Gut ◽  
Metabolic Switch ◽  
Human Gut Microbiota ◽  
Inflammatory Status

Abstract Fasting is increasingly popular to manage metabolic and inflammatory diseases. Despite the role that the human gut microbiota plays in health and diseases, little is known about its composition and functional capacity during prolonged fasting when the external nutrient supply is reduced or suppressed. We analysed the effects of a 10-d periodic fasting on the faecal microbiota of fifteen healthy men. Participants fasted according to the peer-reviewed Buchinger fasting guidelines, which involve a daily energy intake of about 1046 kJ (250 kcal) and an enema every 2 d. Serum biochemistry confirmed the metabolic switch from carbohydrates to fatty acids and ketones. Emotional and physical well-being were enhanced. Faecal 16S rRNA gene amplicon sequencing showed that fasting caused a decrease in the abundance of bacteria known to degrade dietary polysaccharides such as Lachnospiraceae and Ruminococcaceae. There was a concomitant increase in Bacteroidetes and Proteobacteria (Escherichia coli and Bilophila wadsworthia), known to use host-derived energy substrates. Changes in taxa abundance were associated with serum glucose and faecal branched-chain amino acids (BCAA), suggesting that fasting-induced changes in the gut microbiota are associated with host energy metabolism. These effects were reversed after 3 months. SCFA levels were unchanged at the end of the fasting. We also monitored intestinal permeability and inflammatory status. IL-6, IL-10, interferon γ and TNFα levels increased when food was reintroduced, suggesting a reactivation of the postprandial immune response. We suggest that changes in the gut microbiota are part of the physiological adaptations to a 10-d periodic fasting, potentially influencing its beneficial health effects.

scholarly journals The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile

2020 ◽  
Vol 8 (5) ◽  
pp. 677 ◽  
Author(s):  
Monique J. T. Crobach ◽  
Quinten R. Ducarmon ◽  
Elisabeth M. Terveer ◽  
Celine Harmanus ◽  
Ingrid M. J. G. Sanders ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Clostridioides Difficile ◽  
Bacterial Microbiota ◽  
Differential Abundance Analysis ◽  
Gut Microbiota Composition ◽  
Eubacterium Hallii

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p < 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients’ gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.

scholarly journals Plasma Metabolites Related to Peripheral and Hepatic Insulin Sensitivity Are Not Directly Linked to Gut Microbiota Composition

Nutrients ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 2308
Author(s):  
Annefleur M. Koopen ◽  
Nicolien C. de Clercq ◽  
Moritz V. Warmbrunn ◽  
Hilde Herrema ◽  
Mark Davids ◽  
...  
Keyword(s):  
Insulin Sensitivity ◽  
Gut Microbiota ◽  
Prediction Models ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Plasma Metabolites ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Cross Sectional ◽  
Gut Microbiota Composition

Plasma metabolites affect a range of metabolic functions in humans, including insulin sensitivity (IS). A subset of these plasma metabolites is modified by the gut microbiota. To identify potential microbial–metabolite pathways involved in IS, we investigated the link between plasma metabolites, gut microbiota composition, and IS, using the gold-standard for peripheral and hepatic IS measurement in a group of participants with metabolic syndrome (MetSyn). In a cross-sectional study with 115 MetSyn participants, fasting plasma samples were collected for untargeted metabolomics analysis and fecal samples for 16S rRNA gene amplicon sequencing. A two-step hyperinsulinemic euglycemic clamp was performed to assess peripheral and hepatic IS. Collected data were integrated and potential interdependence between metabolites, gut microbiota, and IS was analyzed using machine learning prediction models. Plasma metabolites explained 13.2% and 16.7% of variance in peripheral and hepatic IS, respectively. Fecal microbiota composition explained 4.2% of variance in peripheral IS and was not related to hepatic IS. Although metabolites could partially explain the variances in IS, the top metabolites related to peripheral and hepatic IS did not significantly correlate with gut microbiota composition (both on taxonomical level and alpha-diversity). However, all plasma metabolites could explain 18.5% of the variance in microbial alpha-diversity (Shannon); the top 20 metabolites could even explain 44.5% of gut microbial alpha-diversity. In conclusion, plasma metabolites could partially explain the variance in peripheral and hepatic IS; however, these metabolites were not directly linked to the gut microbiota composition, underscoring the intricate relation between plasma metabolites, the gut microbiota, and IS in MetSyn

scholarly journals The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Mohanraj Gunasekaran ◽  
Maya Lalzar ◽  
Yehonatan Sharaby ◽  
Ido Izhaki ◽  
Malka Halpern
Keyword(s):  
Secondary Metabolites ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Amplicon Sequencing ◽  
Control Group ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Degrading Bacteria ◽  
And Control ◽  
Gut Microbiota Composition

AbstractSunbirds feed on tobacco tree nectar which contains toxic nicotine and anabasine secondary metabolites. Our aim was to understand the effect of nicotine and anabasine on the gut microbiota composition of sunbirds. Sixteen captive sunbirds were randomly assigned to two diets: artificial nectar either with (treatment) or without (control) added nicotine and anabasine. Excreta were collected at 0, 2, 4 and 7 weeks of treatment and samples were processed for bacterial culture and high-throughput amplicon sequencing of the 16S rRNA gene. The gut microbiome diversity of the treated and control birds changed differently along the seven-week experiment. While the diversity decreased in the control group along the first three samplings (0, 2 and 4 weeks), it increased in the treatment group. The microbiota composition analyses demonstrated that a diet with nicotine and anabasine, significantly changed the birds’ gut microbiota composition compared to the control birds. The abundance of nicotine- and anabasine- degrading bacteria in the excreta of the treated birds, was significantly higher after four and seven weeks compared to the control group. Furthermore, analysis of culturable isolates, including Lactococcus, showed that sunbirds’ gut-associated bacteria were capable of degrading nicotine and anabasine, consistent with their hypothesised role as detoxifying and nutritional symbionts.

Sign in / Sign up

Export Citation Format

Share Document