Drastic Effects on the Microbiome of a Young Rower Engaged in High-Endurance Exercise After a Month Usage of a Dietary Fiber Supplement

Food supplements are increasingly used worldwide. However, research on the efficacy of such supplements on athlete's well-being and optimal sports performance is very limited. This study performed in junior academic rowing explores the effects of nutritional supplements to aid to the high energy requirements at periods of intense exercise. Herein, the effects of prebiotic fibers on the intestinal microbiome composition of an 18-year-old athlete exercising at high loads during an 8-month period in a “real-life” setting were examined using next-generation sequencing analysis. Results demonstrated that although the alpha diversity of the subject's microbiome drastically decreased [from 2.11 precompetition to 1.67 (p < 0.05)] upon fiber consumption, the Firmicutes/Bacteroidetes ratio increased significantly [from 3.11 to 4.55, as compared with population average (p < 0.05)]. Underlying these macrolevel microbial alterations were demonstrable shifts from acetate- to butyrate-producing bacteria, although with stable effects on the Veillonella species. To our knowledge, this a unique study that shows pronounced changes in the gut microbiome of the young athlete at the competition season and their favorable compensation by the dietary fiber intake. The data here expand the overall understanding of how the high energy needs in high-intensity sports like academic rowing could be supported by dietary fiber supplement consumption.

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Dietary Protein, Fiber and Coffee Are Associated with Small Intestine Microbiome Composition and Diversity in Patients with Liver Cirrhosis

Nutrients ◽

10.3390/nu12051395 ◽

2020 ◽

Vol 12 (5) ◽

pp. 1395 ◽

Cited By ~ 1

Author(s):

Shehnaz K. Hussain ◽

Tien S. Dong ◽

Vatche Agopian ◽

Joseph R. Pisegna ◽

Francisco A. Durazo ◽

...

Keyword(s):

Liver Cirrhosis ◽

Diet Quality ◽

Alpha Diversity ◽

Healthy Eating Index ◽

Sequencing Data ◽

Microbiome Composition ◽

Coffee Drinking ◽

Microbial Profile ◽

Protein Fiber ◽

Fiber Consumption

The gut microbiome is a key factor in chronic liver disease progression. In prior research, we found that the duodenal microbiome was associated with sex, ethnicity, and cirrhosis complications. Here, we examined the association between diet and the duodenal microbiome in patients with liver cirrhosis. This study included 51 participants who completed a detailed food frequency questionnaire and donated duodenal biopsies for microbiome characterization by 16S ribosomal RNA gene sequencing. Data were analyzed for alpha diversity, beta diversity, and association of taxa abundance with diet quality and components using QIIME 2 pipelines. Diet quality was assessed through calculation of the Healthy Eating Index 2010. Participants with higher adherence to protein recommendations exhibited increased microbial richness and evenness (p = 0.03) and a different microbial profile compared to those with lower adherence (p = 0.03). Prevotella-9 and Agathobacter were increased in association with increased protein adherence. Fiber consumption was also associated with the duodenal microbial profile (p = 0.01), with several taxa exhibiting significantly decreased or increased abundance in association with fiber intake. Coffee drinking was associated with microbial richness and evenness (p = 0.001), and there was a dose–response association between coffee drinking and relative abundance of Veillonella (p = 0.01). We conclude that protein, fiber, and coffee are associated with diversity and composition of the duodenal microbiome in liver cirrhosis.

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Pancreatic cancer intratumoral microbiome and characteristics within paired patient samples.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.4_suppl.744 ◽

2020 ◽

Vol 38 (4_suppl) ◽

pp. 744-744

Author(s):

Sonal Suresh Noticewala ◽

Daniel Lin ◽

Ramez Kouzy ◽

Anirban Maitra ◽

Lauren Elizabeth Colbert ◽

...

Keyword(s):

Pancreatic Cancer ◽

Beta Diversity ◽

Pancreatic Tumor ◽

Bacterial Species ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Sequencing Analysis ◽

Normal Pancreas ◽

16S Sequencing ◽

Resected Tumor

744 Background: While most studies evaluating the microbiome in gastrointestinal cancers analyze stool, little is known about the microbiota of the peri-tumoral and intra-tumoral environment. Here, we evaluated the intra-tumoral and peri-tumoral (duodenum and normal pancreas) microbiome for paired duodenal, normal pancreas and resected tumor specimens from pancreatic cancer patients. The purpose of this study was to describe the similarities and differences within patient microbiota. Methods: Fifteen specimens from 5 patients with pancreatic cancer were collected during surgical resection. Genomic bacterial DNA was extracted from these specimens and underwent 16S rRNA sequencing. Alpha (Inverse Simpson) and beta diversity were calculated, and relative abundances of individual bacterial species were compared. Sorensen distance was used the evaluate the spread in beta diversity between paired sample types. Results: Of the five patients who underwent resection, the following baseline characteristics were obtained: median age = 65 years (range 55 -80 years), 2/5 patients were treated with gemcitabine/abraxane, 3/5 patients were treated with oxaliplatin, irinotecan, fluorouracil, and leucovorin (FOLFIRINOX); 4/5 patients received pre-operative radiation. 16s sequencing analysis of the pancreatic tumor showed the dominant genus to be Escherichia/Shigella (10.6%). Bradyrhizobium (10.1 %) was dominant in the normal pancreas . Escherichia/Shigella (14.3%) was abundant in the duodenum. There was a trend towards higher alpha diversity in tumor vs. normal duodenum/ pancreas (p = 0.12). Sorensen distance was statistically different between sample types (p = 0.004), with duodenal samples most consistent (distance = 67.82), and tumor vs. normal pancreas (81.86) and tumor vs. other tumor samples the most heterogeneous (78.5). Conclusions: This pilot data suggests that the pancreatic tumor microbiome is distinct from the normal pancreas and duodenal microbiome, which indicates tumor specific bacteria should be studied. In future studies, intra-tumoral microbiome may be more relevant to associations with outcomes and treatment response than stool or intestinal microbiome studies.

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Diet Modification and Not Timed Feeding Strategies Result in Intestinal Microbiome Alterations (P21-030-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz041.p21-030-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Cited By ~ 1

Author(s):

Marie van der Merwe ◽

Sunita Sharma ◽

Jade Caldwell ◽

Nicholas Smith ◽

Richard Bloomer ◽

...

Keyword(s):

High Fat Diet ◽

Beta Diversity ◽

Diversity Index ◽

Alpha Diversity ◽

Taxonomic Composition ◽

Intestinal Microbiome ◽

Feeding Strategies ◽

High Fat ◽

Microbiome Composition ◽

Intestinal Length

Abstract Objectives Time-restricted feeding strategies have been shown to normalize obesity parameters, even under high fat feeding conditions. The objective of this study is to examine whether timed feeding alters parameters of gut health or intestinal microbiome composition. Methods C57BL/6 male mice were randomized to Chow or a high fat diet (HFD) for 6 weeks, followed by a switch from HFD to 1) Chow (sChow), 2) Purified Vegan – Daniel Fast (DF), 3) HFD ad lib, 4) HFD time restricted (TRF), 5) HFD alternative day fasting (ADF), or 6) HFD 60% caloric restriction (CR) for an additional 8 weeks. Results We observed that body mass gain was reduced for all intervention groups (P ≤ 0.0001). Small intestinal length and cecal weight were increased in Chow, sChow and DF (P ≤ 0.02), while total cecal short chain fatty acid (SCFA) concentration was non-significantly increased for all groups consuming the HFD. Proprionate was specifically increased in the Chow, sChow and DF groups (P ≤ 0.02). Chow fed microbiota remained stable in taxonomic composition and alpha diversity (Shannon diversity index) throughout the study. HF fed microbiota displayed lower alpha diversity along with reduced phylum levels of Bacteroidetes and increase Firmicutes. Animals switched from HF to Chow demonstrated a rapid transition in taxonomic composition, alpha, and beta diversity that initially resembled HF, but clustered closely with Chow by weeks 4 and 8 of intervention. After 8 weeks on the respective dietary protocols, alpha diversity of the DF was most similar to Chow fed animals and also resulted in the largest increase in Bacteriodetes and largest decrease in Firmicutes. Beta diversity (weighted UniFrac) showed Chow, sChow, and DF clustered together, while high fat fed groups (HF, CR, ADF, and TRF) clustered. Compared with HF controls, CR and TRF led to a relative increase in the classes Clostridia, Deferribacteres and Deltaproteobacteria. The taxonomic composition and alpha diversity of ADF fasting resembled HF under fed conditions, while ADF under fasting conditions more closely resembled CR and TRF. Conclusions In conclusion, timed feeding on a high fat diet did not result in significant changes in the microbiome, demonstrating that diet, and not fasting is the major determinant for microbiome composition. Funding Sources University of Memphis & Children's Foundation Research Institute, Memphis.

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Application of Clustering Method to Explore the Correlation Between Dominant Flora and the Autism Spectrum Disorder Clinical Phenotype in Chinese Children

Frontiers in Neuroscience ◽

10.3389/fnins.2021.760779 ◽

2021 ◽

Vol 15 ◽

Author(s):

Biyuan Chen ◽

Na You ◽

Bangquan Pan ◽

Xueyi He ◽

Xiaobing Zou

Keyword(s):

Autism Spectrum Disorder ◽

Southern China ◽

Repetitive Behavior ◽

Alpha Diversity ◽

Cross Sectional Study ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Intestinal Microbiome ◽

Cross Sectional ◽

Microbiome Composition

Autism spectrum disorder (ASD) is characterized by deficits in social interactions and repetitive, stereotypic behaviors. Evidence shows that bidirectional communication of the gut-brain axis plays an important role. Here, we recruited 62 patients with ASD in southern China, and performed a cross-sectional study to test the relationship between repeated behavior, gut microbiome composition, and alpha diversity. We divided all participants into two groups based on the clustering results of their microbial compositions and found Veillonella and Ruminococcus as the seed genera in each group. Repetitive behavior differed between clusters, and cluster 2 had milder repetitive symptoms than Cluster 1. Alpha diversity between clusters was significantly different, indicating that cluster 1 had lower alpha diversity and more severe repetitive, stereotypic behaviors. Repetitive behavior had a negative correlation with alpha diversity. We demonstrated that the difference in intestinal microbiome composition and altered alpha diversity can be associated with repetitive, stereotypic behavior in autism. The role of Ruminococcus and Veillonella in ASD is not yet understood.

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Gastroesophageal Reflux Type and Number Correlate with Nutritional Patterns (P06-066-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz031.p06-066-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Sergey Morozov ◽

Vasily Kropochev ◽

Vasily Isakov

Keyword(s):

Gastroesophageal Reflux ◽

Dietary Fiber ◽

High Energy ◽

Weak Acid ◽

Esophageal Acid Exposure ◽

Acid Exposure ◽

Energy Value ◽

Esophageal Ph ◽

Medium Strength ◽

Fiber Consumption

Abstract Objectives The correlation of nutritional patterns with number and types of gastroesophageal refluxes is poorly studied yet. Aim: To assess the effect of actual nutrition of GERD patients on the number and type of gastroesophageal reflux detected with 24-hours esophageal pH-impedance. Methods One hundred twenty-four GERD patients (54 men, age (M ± m): 46 ± 17.7 y.o., BMI 28.5 ± 0.6 kg/m2) and 41 healthy controls (8 men, age 42 ± 12.4 y.o., BMI 28.3 ± 1.3 kg/m2) were examined with the use of language-specific food frequency questionnaire and 24-hours esophageal pH-impedance (Ohmega, MMS; 2 pH, 6 impedance catheters, Unisensor). The correlation analysis between macro- and micronutrient consumption and the number of gastroesophageal refluxes (GER), their acidity and duration was performed (Statistica 10, StatSoft) Results Direct medium-strength correlation was found between esophageal acid exposure time and the energy value of the ration (Spearman rank R = 0.19, p < 0.05), and the amount of consumed fat (R = 0.2, p < 0.05). There was a direct correlation of the total number of GERs with the energy value of the ration (R = 0.35, p < 0.05), protein (R = 0.3, p < 0.05), fat (R = 0.33, p < 0.05), and alcohol consumption (R = 0.28, p < 0.05) and the inverse one with the dietary fiber consumption (R = −0.22). Significant direct correlation was found between the number of acid GERs and total energy value of the ration (R = 0.35, p < 0.05), consumption of fat (R = 0.32, p < 0.05), protein (R = 0.25, p < 0.05), carbohydrates (R = 0.24, p < 0.05) and alcohol (R = 0.24, p < 0.05). Number of weak-acid GERs showed direct correlation with the calories intake (R = 0.22, p < 0.05), fat (R = 0.21, p < 0.05), protein (R = 0.22, p < 0.05), alcohol (R = 0.23, p < 0.05) consumption, and the inverse one with the amount of dietary fiber intake (R = −0.24, p < 0.05). Number of high GERs correlated directly with the amount of fat (R = 0.3, p < 0.05), protein (R = 0.22, p < 0.05), alcohol (R = 0.25, p < 0.05) consumed, and inversely with the amount of dietary fiber (R = −0.25, p < 0.05) in the ration. Paired comparison of the correlation coefficients was performed, but didn't reveal any difference. Conclusions High energy value, consumption of fat and alcohol showed direct medium-strength correlation with esophageal acid exposure and number of GERs. Dietary fiber consumption correlated inversely with total number, weak acid and high GERs. Funding Sources Federal research Center of Nutrition and Biotechnology, Russian science foundation.

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Hirschsprung’s Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome

Case Reports in Pediatrics ◽

10.1155/2018/3292309 ◽

2018 ◽

Vol 2018 ◽

pp. 1-6

Author(s):

Georg Singer ◽

Karl Kashofer ◽

Christoph Castellani ◽

Holger Till

Keyword(s):

Hirschsprung's Disease ◽

Hirschsprung’S Disease ◽

Gene Sequencing ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Sequencing Analysis ◽

Fecal Microbiome ◽

Probiotic Treatment ◽

Pull Through ◽

Generation Sequencing

Approximately 40% of children with Hirschsprung’s disease (HD) suffer from Hirschsprung’s associated enterocolitis (HAEC) despite correct surgery. Disturbances of the intestinal microbiome may play a role. Treatment with probiotics based on individual analyses of the fecal microbiome has not been published for HD patients with recurrent HAEC yet. A boy with trisomy 21 received transanal pull-through at the age of 6 months for rectosigmoid HD. With four years, he suffered from recurrent episodes of HAEC. The fecal microbiome was measured during three healthy and three HAEC episodes by next-generation sequencing. The patient was started on daily probiotics for 3 months; the fecal microbiome was measured weekly. The fecal microbiome differed significantly between healthy and HAEC episodes. HAEC episodes were associated with significant decreases of Actinobacteria and significant increases of Bacteroidetes and Proteobacteria. Probiotic treatment led to a significant increase of alpha diversity and a significant increase of Bifidobacterium and Streptococcus as well as decreases of Rikenellaceae, Pseudobutyrivibrio, Blautia, and Lachnospiraceae. A longitudinal observation of the microbiome has never been performed following correction of Hirschsprung’s disease. Probiotic treatment significantly changed the fecal microbiome; the alterations were not limited to strains contained in the administered probiotics.

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Quantifying technical confounders in microbiome studies

Cardiovascular Research ◽

10.1093/cvr/cvaa128 ◽

2020 ◽

Cited By ~ 2

Author(s):

Theda U P Bartolomaeus ◽

Till Birkner ◽

Hendrik Bartolomaeus ◽

Ulrike Löber ◽

Ellen G Avery ◽

...

Keyword(s):

Dna Extraction ◽

Human Microbiome ◽

Alpha Diversity ◽

Extraction Methods ◽

Intestinal Microbiome ◽

Interindividual Differences ◽

Microbiome Composition ◽

Technical Developments ◽

Dna Extraction Methods ◽

The Impact

Abstract Aims Recent technical developments have allowed the study of the human microbiome to accelerate at an unprecedented pace. Methodological differences may have considerable impact on the results obtained. Thus, we investigated how different storage, isolation, and DNA extraction methods can influence the characterization of the intestinal microbiome, compared to the impact of true biological signals such as intraindividual variability, nutrition, health, and demographics. Methods and results An observative cohort study in 27 healthy subjects was performed. Participants were instructed to collect stool samples twice spaced by a week, using six different methods (naive and Zymo DNA/RNA Shield on dry ice, OMNIgene GUT, RNALater, 95% ethanol, Zymo DNA/RNA Shield at room temperature). DNA extraction from all samples was performed comparatively using QIAamp Power Fecal and ZymoBIOMICS DNA Kits. 16S rRNA sequencing of the gut microbiota as well as qPCRs were performed on the isolated DNA. Metrics included alpha diversity as well as multivariate and univariate comparisons of samples, controlling for covariate patterns computationally. Interindividual differences explained 7.4% of overall microbiome variability, whereas the choice of DNA extraction method explained a further 5.7%. At phylum level, the tested kits differed in their recovery of Gram-positive bacteria, which is reflected in a significantly skewed enterotype distribution. Conclusion DNA extraction methods had the highest impact on observed microbiome variability, and were comparable to interindividual differences, thus may spuriously mimic the microbiome signatures of various health and nutrition factors. Conversely, collection methods had a relatively small influence on microbiome composition. The present study provides necessary insight into the technical variables which can lead to divergent results from seemingly similar study designs. We anticipate that these results will contribute to future efforts towards standardization of microbiome quantification procedures in clinical research.

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Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion

Scientific Reports ◽

10.1038/s41598-021-95992-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lama Nazzal ◽

Fritz Francois ◽

Nora Henderson ◽

Menghan Liu ◽

Huilin Li ◽

...

Keyword(s):

Kidney Stones ◽

Stone Formation ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Urinary Oxalate ◽

Treatment Groups ◽

The Us ◽

Urine Electrolytes ◽

H Pylori ◽

Urinary Oxalate Excretion

AbstractThe incidence of kidney stones is increasing in the US population. Oxalate, a major factor for stone formation, is degraded by gut bacteria reducing its intestinal absorption. Intestinal O. formigenes colonization has been associated with a lower risk for recurrent kidney stones in humans. In the current study, we used a clinical trial of the eradication of Helicobacter pylori to assess the effects of an antibiotic course on O. formigenes colonization, urine electrolytes, and the composition of the intestinal microbiome. Of 69 healthy adult subjects recruited, 19 received antibiotics for H. pylori eradication, while 46 were followed as controls. Serial fecal samples were examined for O. formigenes presence and microbiota characteristics. Urine, collected serially fasting and following a standard meal, was tested for oxalate and electrolyte concentrations. O. formigenes prevalence was 50%. Colonization was significantly and persistently suppressed in antibiotic-exposed subjects but remained stable in controls. Urinary pH increased after antibiotics, but urinary oxalate did not differ between the control and treatment groups. In subjects not on antibiotics, the O. formigenes-positive samples had higher alpha-diversity and significantly differed in Beta-diversity from the O. formigenes-negative samples. Specific taxa varied in abundance in relation to urinary oxalate levels. These studies identified significant antibiotic effects on O. formigenes colonization and urinary electrolytes and showed that overall microbiome structure differed in subjects according to O. formigenes presence. Identifying a consortium of bacterial taxa associated with urinary oxalate may provide clues for the primary prevention of kidney stones in healthy adults.

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Next-Generation Sequencing Analysis of the Tineola bisselliella Larval Gut Transcriptome Reveals Candidate Enzymes for Keratin Digestion

Genes ◽

10.3390/genes12081113 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1113

Author(s):

Michael Schwabe ◽

Sven Griep ◽

Henrike Schmidtberg ◽

Rudy Plarre ◽

Alexander Goesmann ◽

...

Keyword(s):

Next Generation Sequencing ◽

Disulfide Bonds ◽

Differentially Expressed ◽

Intestinal Microbiome ◽

Sequencing Analysis ◽

High Quality ◽

Transcriptomic Data ◽

Next Generation Sequencing Analysis ◽

Generation Sequencing ◽

Tineola Bisselliella

The clothes moth Tineola bisselliella is one of a few insects that can digest keratin, leading to the destruction of clothing, textiles and artwork. The mechanism of keratin digestion is not yet fully understood, partly reflecting the lack of publicly available genomic and transcriptomic data. Here we present a high-quality gut transcriptome of T. bisselliella generated from larvae reared on keratin-rich and keratin-free diets. The overall transcriptome consists of 428,221 contigs that were functionally annotated and screened for candidate enzymes involved in keratin utilization. As a mechanism for keratin digestion, we identified cysteine synthases, cystathionine β-synthases and cystathionine γ-lyases. These enzymes release hydrogen sulfite, which may reduce the disulfide bonds in keratin. The dataset also included 27 differentially expressed contigs with trypsin domains, among which 20 were associated with keratin feeding. Finally, we identified seven collagenases that were upregulated on the keratin-rich diet. In addition to this enzymatic repertoire potentially involved in breaking down keratin, our analysis of poly(A)-enriched and poly(A)-depleted transcripts suggested that T. bisselliella larvae possess an unstable intestinal microbiome that may nevertheless contribute to keratin digestion.

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Gut Microbiome in Psoriasis: An Updated Review

Pathogens ◽

10.3390/pathogens9060463 ◽

2020 ◽

Vol 9 (6) ◽

pp. 463

Author(s):

Mariusz Sikora ◽

Albert Stec ◽

Magdalena Chrabaszcz ◽

Aleksandra Knot ◽

Anna Waskiel-Burnat ◽

...

Keyword(s):

Gut Microbiome ◽

Beta Diversity ◽

Large Scale ◽

Skin Diseases ◽

Intestinal Barrier ◽

Alpha Diversity ◽

Current Data ◽

Intestinal Microbiome ◽

Microbial Composition ◽

Alpha And Beta Diversity

(1) Background: A growing body of evidence highlights that intestinal dysbiosis is associated with the development of psoriasis. The gut–skin axis is the novel concept of the interaction between skin diseases and microbiome through inflammatory mediators, metabolites and the intestinal barrier. The objective of this study was to synthesize current data on the gut microbial composition in psoriasis. (2) Methods: We conducted a systematic review of studies investigating intestinal microbiome in psoriasis, using the PRISMA checklist. We searched MEDLINE, EMBASE, and Web of Science databases for relevant published articles (2000–2020). (3) Results: All of the 10 retrieved studies reported alterations in the gut microbiome in patients with psoriasis. Eight studies assessed alpha- and beta-diversity. Four of them reported a lack of change in alpha-diversity, but all confirmed significant changes in beta-diversity. At the phylum-level, at least two or more studies reported a lower relative abundance of Bacteroidetes, and higher Firmicutes in psoriasis patients versus healthy controls. (4) Conclusions: There is a significant association between alterations in gut microbial composition and psoriasis; however, there is high heterogeneity between studies. More unified methodological standards in large-scale studies are needed to understand microbiota’s contribution to psoriasis pathogenesis and its modulation as a potential therapeutic strategy.

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