scholarly journals Changes in the Human Gut Microbiota Associated With Colonization by Blastocystis sp. and Entamoeba spp. in Non-Industrialized Populations

2021 ◽  
Vol 11 ◽  
Author(s):  
Gaël Even ◽  
Ana Lokmer ◽  
Jules Rodrigues ◽  
Christophe Audebert ◽  
Eric Viscogliosi ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Experimental Studies ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Sequencing Data ◽  
Human Gut ◽  
Bacterial Microbiota ◽  
Bacterial Microbiome ◽  
Blastocystis Sp

Human gut microbial communities are mainly composed of bacteria, but also include fungi, viruses, archaea, and protozoa, whose role in the gut ecosystem has only recently begun to be recognized. For example, humans colonized by Blastocystis (a gut protozoan with controversial pathogenicity) host a more diverse bacterial microbiota than individuals not carrying it, suggesting that its presence may be beneficial for the host. In parallel, the presence of non-pathogenic Entamoeba spp. has been associated with an increased diversity and compositional shifts in the bacterial microbiota of healthy rural individuals in Cameroon. However, Entamoeba and Blastocystis, the two most prevalent human gut protozoa, have never been studied in the same individuals, preventing the study of their interaction. As Blastocystis is one of the few gut protozoa commonly found in industrialized populations, which are otherwise mostly devoid of gut eukaryotes, we need to focus on rural “traditional” populations, who harbor a higher diversity of gut eukaryotes (whether pathogenic or commensal) in order to study protozoa interactions in the gut ecosystem. To this end, we profiled the gut bacterial microbiota of 134 healthy Cameroonian adults using 16S rRNA gene amplicon sequencing data. Entamoeba and Blastocystis presence and co-occurrence pattern in the same individuals were determined using metagenomic shotgun data. We found that, when taking into account both protozoa jointly, Blastocystis was associated with both a higher richness and a higher evenness of the gut bacterial microbiota, while Entamoeba was associated only with a higher richness. We demonstrated a cumulative influence of these protozoa on bacterial microbiome diversity. Furthermore, while the abundance of several common taxa (for example, Ruminococcaceae, Coprococcus and Butyrivibrio) varied according to Blastocystis colonization, only a single Bacteroides amplicon sequence variant was found to be differentially abundant between Entamoeba-negative and Entamoeba-positive samples. Given the specific signature of each protozoan on the gut microbiota and the seemingly stronger association for Blastocystis, our results suggest that Blastocystis and Entamoeba interact with gut bacteria each in its own way, but experimental studies are needed to explore the precise mechanisms of these interactions.

scholarly journals Optimisation of sample storage and DNA extraction for human gut microbiota studies​

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jekaterina Kazantseva ◽  
Esther Malv ◽  
Aleksei Kaleda ◽  
Aili Kallastu ◽  
Anne Meikas
Keyword(s):  
Gut Microbiota ◽  
Dna Extraction ◽  
Personalised Medicine ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Sequencing Technologies ◽  
Different Temperatures ◽  
Reliable Solution

Abstract Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

scholarly journals Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment

2019 ◽  
Vol 7 (7) ◽  
pp. 209 ◽  
Author(s):  
Juline M. Walter ◽  
Andrea Bagi ◽  
Daniela M. Pampanin
Keyword(s):  
Gut Microbiota ◽  
Marine Environment ◽  
Gut Microbiome ◽  
Atlantic Cod ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Comparison Results ◽  
Southern Norway ◽  
Microbial Groups

Background: Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed in those studies, we hypothesized that certain microbial groups in the gut can serve as indicators of pollution. To test this hypothesis, we explored the possibility of identifying key microbial players that indicate environmental contamination. Methods: Published 16S rRNA gene amplicon sequencing data generated from the gut microbiota of Atlantic cod caught in geographically different Norwegian waters were used for bacterial diversity comparison. Results: Different microbiomes were identified between the northern Norway and southern Norway samples. Several bacterial genera previously identified as polycyclic aromatic hydrocarbon degraders were present only in the samples collected in the southern Norway area, suggesting fish contamination with oil-related compounds. Conclusions: The results contribute to the identification of bacterial taxa present in the Atlantic cod gut that indicate fish exposure to contaminants in the marine environment.

scholarly journals An extended reconstruction of human gut microbiota metabolism of dietary compounds

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Telmo Blasco ◽  
Sergio Pérez-Burillo ◽  
Francesco Balzerani ◽  
Daniel Hinojosa-Nogueira ◽  
Alberto Lerma-Aguilera ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Metabolic Networks ◽  
16S Rrna Gene Sequencing ◽  
Complex Problem ◽  
Rrna Gene ◽  
Limited Information ◽  
Sequencing Data ◽  
Human Gut ◽  
Human Gut Microbiota

AbstractUnderstanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.

scholarly journals Characterization of Gut Microbiota Associated with Clinical Parameters in Intrahepatic Cholestasis of Pregnant Patients

2019 ◽  
Author(s):  
Rong Li ◽  
xuehai chen ◽  
Zhongzhen Liu ◽  
Yan Chen ◽  
Chuan Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Pregnant Women ◽  
Intrahepatic Cholestasis ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Clinical Parameters ◽  
Sequencing Data ◽  
Unifrac Distance ◽  
Biochemical Indices ◽  
And Control

Abstract BackgroundIntrahepatic cholestasis of pregnancy (ICP) is a liver disease that specifically occurs during pregnancy. Pregnant women with ICP biochemically reflect elevated liver functions and increases in serum bilirubin levels, while clinically individuals can display symptoms of itching and have elevated risks of preterm delivery and stillbirths. We hypothesized that there linkages between gut microbiota and ICP progression exist and could be scientifically characterized. MethodsIn total, 27 patients with ICP and 31 unafflicted control patients were recruited in this study. We performed 16S rRNA gene amplicon sequencing on gut microbiota from individual fecal samples. Sequencing data was analyzed and the correlations between components of microbiota and patient ICP status were tested. Relative abundances, related metabolic pathways, and significantly different OTUs between ICP and control patients were identified.ResultsBiochemical indices including measures for bile, ALT, AST, Dbil, and Tbil, and these were found to at higher levels in ICP versus control patients. Gut microbiota in pregnant women was dominated by four major phyla and 27 core genera. PCoA analysis results indicated that there was marginal significant clustering in unweighted Unifrac distance matrices. A moderate correlation coefficient was observed between specific OTUs and measured clinical parameters of patients. When comparing relatively rare microbiota taxa, the abundance of Butyricimonas was lower, while Citrobacter, Pseudomonas, Streptococcus, and Weissella were higher in ICP patients than in control patients. No significant differences in the pathways between ICP and control patients were identified.ConclusionsOur research indicated that patients with ICP have altered phylogenetic gut microbiota profiles compared to control patients without ICP, and that the composition was associated with measurements of patient clinical parameters. These alterations may be correlated with variations of the levels of patient enteric bile acids, and may play a role in the progression of ICP.

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 Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

scholarly journals Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lito E. Papanicolas ◽  
Sarah K. Sims ◽  
Steven L. Taylor ◽  
Sophie J. Miller ◽  
Christos S. Karapetis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Haematological Malignancy ◽  
Amplicon Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Conventional Chemotherapy ◽  
Myelosuppressive Chemotherapy ◽  
Gram Positive Bacteria ◽  
Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

scholarly journals Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice

Metabolites ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 482
Author(s):  
Jae-Kwon Jo ◽  
Seung-Ho Seo ◽  
Seong-Eun Park ◽  
Hyun-Woo Kim ◽  
Eun-Ju Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
High Fat Diet ◽  
Amplicon Sequencing ◽  
Gas Chromatography Mass Spectrometry ◽  
Control Group ◽  
Rrna Gene ◽  
High Fat ◽  
Underlying Mechanisms ◽  
Insight Into

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

scholarly journals SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Clarisse Marotz ◽  
Pedro Belda-Ferre ◽  
Farhana Ali ◽  
Promi Das ◽  
Shi Huang ◽  
...  
Keyword(s):  
Health Care Providers ◽  
Rna Virus ◽  
Bacterial Community Composition ◽  
Hospital Setting ◽  
Amplicon Sequencing ◽  
Hospital Environment ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Care Providers ◽  
Single Amplicon

Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment.

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