The Fermented Soy Beverage Q-CAN® Plus Induces Beneficial Changes in the Oral and Intestinal Microbiome

Abstract Background Q-CAN® Plus is a pasteurized soy fermented product rich in isoflavones that has been used for over 30 years to aid in recovery from a wide range of conditions. Objectives To identify the changes in the oral and fecal microbiome in lean and obese subjects due to consumption of Q-CAN®, and to assess the expected consequences of these changes based on the published literature. Methods Prospective study of lean (10) and obese (9) subjects consuming Q-CAN® twice daily for 4 weeks with 8 weeks follow-up. Microbial DNA was extracted from saliva and stool samples, amplified against the V4 region of the 16S ribosomal RNA gene and data analyzed using QIIME 1.9.1 bioinformatics. 440 samples were collected in total, 424 of which were productive and yielded good quality data. Results STOOL. In the lean population Bifidobacteria and Blautia show a significant increase while taking Q-CAN®, and there was a trend for this in the obese population. ORAL. There were relatively fewer major changes in the oral microbiome with an increase in the family Veillonellaceae in the lean population while on Q-CAN®. Conclusion Q-CAN® consumption induced a number of significant changes in the fecal and oral microbiome. Most notably an increase in the stool microbiome of Bifidobacteria and Blautia, both of which are associated with positive health benefits, and in the saliva an increase in Veillonellaceae.

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The Fermented Soy Beverage Q-CAN® Plus Induces Beneficial Changes in the Oral and Intestinal Microbiome

10.21203/rs.3.rs-22397/v1 ◽

2020 ◽

Author(s):

Evangelos Dioletis ◽

Ricardo Paiva ◽

Eleanna Kaffe ◽

Eric R. Secor ◽

Theresa R. Weiss ◽

...

Keyword(s):

Oral Microbiome ◽

Intestinal Microbiome ◽

Quality Data ◽

Positive Health ◽

Fecal Microbiome ◽

Fermented Product ◽

Wide Range ◽

Obese Subjects ◽

Stool Samples ◽

Microbial Dna

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The Fermented Soy Beverage Q-CAN® Plus Induces Beneficial Changes in the Oral and Intestinal Microbiome

10.21203/rs.3.rs-26827/v2 ◽

2020 ◽

Author(s):

Evangelos Dioletis ◽

Ricardo Paiva ◽

Eleanna Kaffe ◽

Eric R. Secor ◽

Theresa R. Weiss ◽

...

Keyword(s):

Oral Microbiome ◽

Intestinal Microbiome ◽

Quality Data ◽

Positive Health ◽

Fecal Microbiome ◽

The Family ◽

Stool Samples ◽

Microbial Dna ◽

Good Quality Data

Abstract Background: Soy products are associated with many beneficial health consequences, but their effects on the human intestinal microbiome are poorly characterized. Objectives: To identify the changes in the oral and fecal microbiome in lean and obese participants due to consumption of Q-CAN®, and to assess the expected consequences of these changes based on the published literature. Methods: Prospective study of lean (10) and obese (9) participants consuming Q-CAN® twice daily for 4 weeks with 8 weeks follow-up. Microbial DNA was extracted from saliva and stool samples, amplified against the V4 region of the 16S ribosomal RNA gene and data analyzed using QIIME 1.9.1 bioinformatics. 440 samples were collected in total, 424 of which were productive and yielded good quality data. Results: STOOL. In the lean population Bifidobacteria and Blautia show a significant increase while taking Q-CAN®, and there was a trend for this in the obese population. ORAL. There were relatively fewer major changes in the oral microbiome with an increase in the family Veillonellaceae in the lean population while on Q-CAN®. Conclusion: Q-CAN® consumption induced a number of significant changes in the fecal and oral microbiome. Most notably an increase in the stool microbiome of Bifidobacteria and Blautia, both of which are associated with positive health benefits, and in the saliva an increase in Veillonellaceae. Trial registration: This trial was registered with Clinicaltrials.gov on January 14th 2016. ClinicalTrials.gov Identifier: NCT02656056

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The fermented soy beverage Q-CAN® plus induces beneficial changes in the oral and intestinal microbiome

BMC Nutrition ◽

10.1186/s40795-021-00408-4 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Evangelos Dioletis ◽

Ricardo S. Paiva ◽

Eleanna Kaffe ◽

Eric R. Secor ◽

Theresa R. Weiss ◽

...

Keyword(s):

Oral Microbiome ◽

Intestinal Microbiome ◽

Quality Data ◽

Positive Health ◽

Fecal Microbiome ◽

The Family ◽

Stool Samples ◽

Microbial Dna ◽

Good Quality Data

Abstract Background Soy products are associated with many beneficial health consequences, but their effects on the human intestinal microbiome are poorly characterized. Objectives To identify the changes in the oral and fecal microbiome in lean and obese participants due to consumption of Q-CAN®, and to assess the expected consequences of these changes based on the published literature. Methods Prospective study of lean (10) and obese (9) participants consuming Q-CAN® twice daily for 4 weeks with 8 weeks follow-up. Microbial DNA was extracted from saliva and stool samples, amplified against the V4 region of the 16S ribosomal RNA gene and data analyzed using QIIME 1.9.1 bioinformatics. Four hundred forty-four samples were collected in total, 424 of which were productive and yielded good quality data. Results STOOL. In the lean population Bifidobacteria and Blautia show a significant increase while taking Q-CAN®, and there was a trend for this in the obese population. ORAL. There were relatively fewer major changes in the oral microbiome with an increase in the family Veillonellaceae in the lean population while on Q-CAN®. Conclusion Q-CAN® consumption induced a number of significant changes in the fecal and oral microbiome. Most notably an increase in the stool microbiome of Bifidobacteria and Blautia, both of which are associated with positive health benefits, and in the saliva an increase in Veillonellaceae. Trial registration This trial was registered with Clinicaltrials.gov on January 14th 2016. ClinicalTrials.gov Identifier: NCT02656056

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The Fermented Soy Beverage Q-CAN® Plus Induces Changes in the Oral and Intestinal Microbiome (P20-018-19)

Current Developments in Nutrition ◽

10.1093/cdn/nzz040.p20-018-19 ◽

2019 ◽

Vol 3 (Supplement_1) ◽

Author(s):

Wajahat Mehal ◽

Evangelos Dioletis ◽

Ricardo Paiva ◽

Eric Secor ◽

Theresa Weiss ◽

...

Keyword(s):

Gut Microbiome ◽

Oral Microbiome ◽

Obese Group ◽

Intestinal Microbiome ◽

Quality Data ◽

Metabolic Phenotype ◽

Biological Research ◽

Sequencing Data ◽

Body Type ◽

Lean Group

Abstract Objectives To better understand the mechanisms for the beneficial effects of Q-CAN we identified changes in the fecal and oral microbiome in healthy subjects. Due to the high prevalence of obesity, and the known differences in the microbiome in obesity we want to test the effects on Q-CAN on lean and obese subjects. Methods Prospective study of lean (10) and obese (10) subjects. 11 clinic visits over 14 weeks. 237 ml of soy was dispensed at visit 3 and was consumed twice daily for 4 weeks until visit 7. Visits 8–11 were post treatment. Microbial DNA was extracted from saliva and stool samples, amplified against the V4 region of the 16S ribosomal RNA gene. Raw DNA sequencing data analyzed with the QIIME 1.9.1 bioinformatics pipeline. samples producing > 5000 reads were considered for analysis, and the cutoff abundance was 0.01%. Statistical validation was performed using the SAS software package to calculate Least Squares Means (LSM) and group difference of LSM. 440 samples were collected in total, 424 of which were productive and yielded good quality data. Results STOOL. Obese had higher firmicute/bacteroidetes ratio compared to the lean group. At phylum level the gut microbiome of the obese group shows a trend for decreased firmicute/bacteroidetes ratio while taking Q-CAN. In the lean population actinobacteria show a statistically significant increase (0.0095 ± 0.0039, P = 0.02) during soy consumption compared to baseline. Several genera show a significant decrease in abundance in the obese group upon soy withdrawal including Faecalibacterium, Bifidobacterium and Sutterella. Dorea is increasing in obese group and Lachnospiraceae genus is decreasing in the lean group when comparing samples during consumption to baseline. ORAL. Veillonella and Oribacterium increased during soy consumption vs baseline, while Neisseria is decreasing. Conclusions Fermented soy consumption introduced changes in the abundance of the oral and gut microbiome. The decreasing firmicute to Bacteroidetes ratio is particularly promising as a low ratio is associated with lean body type, while a high ratio is associated with obese body type. The shift in the microbiome in obese individuals may be associated with health benefits such as reduced inflammation, or improvement in the metabolic phenotype. Funding Sources Beso Biological Research, Inc.

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Diet, Serum Short Chain Fatty Acids, and Potential Molecular Associations in Obesity

QJM ◽

10.1093/qjmed/hcab088.006 ◽

2021 ◽

Vol 114 (Supplement_1) ◽

Author(s):

Lobna Mohammad Nabil Helmy ◽

Reem Mohamed Ahmed Sallam ◽

Maha Mohamed Sallam ◽

Hala M Abdelsalam ◽

Dalia Abdel-Wahab Mohamed ◽

...

Keyword(s):

Fatty Acids ◽

Dietary Habits ◽

Short Chain Fatty Acids ◽

Short Chain ◽

Gas Chromatography Mass Spectrometry ◽

Fiber Intake ◽

Positive Health ◽

Wide Range ◽

Obese Subjects ◽

Chain Fatty Acids

Abstract Gut microbiota-derived short-chain fatty acids (SCFAs) have been reported to result in a wide range of health benefits including improvements in body composition and reduced body weight. However, excess production of colonic SCFAs has been implicated in the promotion of obesity. In this study, we aimed to explore the interrelation between diet, SCFAs production and obesity. This study included 31 subjects divided into a lean group and an obese group. Their dietary habits were assessed by means of food-frequency questionnaire and 24-hour recall then blood samples were collected from all of them. Analysis of short-chain fatty acids (i.e., acetate, propionate, and butyrate) in serum was performed using gas chromatography-mass spectrometry (GC-MS). Dietary assessment revealed that obese subjects had a significantly higher intake of carbohydrate, fat and sodium while lean subjects had a significantly higher intake of dietary fiber. Serum levels of propionate were higher in lean subjects compared to obese subjects (P < 0.05). Serum propionate level showed a positive significant correlation with fiber intake (P < 0.05). Our study suggests that healthy dietary choices and increasing daily fiber intake may be associated with positive health outcomes modulated by increasing short chain fatty acids.

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The impact of fixed orthodontic appliances on oral microbiome dynamics in Japanese patients

Scientific Reports ◽

10.1038/s41598-020-78971-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Isamu Kado ◽

Junzo Hisatsune ◽

Keiko Tsuruda ◽

Kotaro Tanimoto ◽

Motoyuki Sugai

Keyword(s):

Relative Abundance ◽

Japanese Patients ◽

Oral Microbiome ◽

Orthodontic Appliances ◽

Periodontal Pathogens ◽

Supragingival Plaque ◽

Fixed Orthodontic Appliances ◽

Microbial Dna ◽

The Impact ◽

Level Analysis

AbstractFixed orthodontic appliances are common and effective tools to treat malocclusion. Adverse effects of these appliances, such as dental caries and periodontitis, may be associated with alteration of the microbiome. This study investigated the impact of these appliances on the dynamics of the oral microbiome. Seventy-one patients were selected. Supragingival plaque samples were collected before placement (T0) and six months after placement (T1). Saliva samples were collected at T0 and T1, and then when appliance removal (T2). Microbial DNA was analyzed by 16S rRNA meta-sequencing. The diversity analysis indicated dynamic changes in the structure of the oral microbiome. Taxonomic analysis at phylum level showed a significant increase in Bacteroidetes and Saccharibacteria (formally TM7) and decrease in Proteobacteria and Actinobacteria over time, in both plaque and saliva. Genus level analysis of relative abundance indicated a significant increase in anaerobic and facultative anaerobes in both plaque and saliva. Fixed orthodontic appliances induced measurable changes in the oral microbiome. This was characterized by an increase in relative abundance of obligate anaerobes, including periodontal pathogens. It can be concluded that this dysbiosis induced by fixed orthodontic appliances is likely to represent a transitional stage in the shift in microbiome from healthy to periodontitis.

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Microbiome ◽

10.1186/s40168-021-01048-3 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Dieter M. Tourlousse ◽

Koji Narita ◽

Takamasa Miura ◽

Mitsuo Sakamoto ◽

Akiko Ohashi ◽

...

Keyword(s):

Dna Extraction ◽

High Throughput Sequencing ◽

Performance Metrics ◽

Collaborative Study ◽

Human Microbiome ◽

Second Phase ◽

Intermediate Precision ◽

Fecal Microbiome ◽

Library Construction ◽

Wide Range

Abstract Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products.

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Modeling Building Stock Development

Sustainability ◽

10.3390/su13020723 ◽

2021 ◽

Vol 13 (2) ◽

pp. 723

Author(s):

Antti Kurvinen ◽

Arto Saari ◽

Juhani Heljo ◽

Eero Nippala

Keyword(s):

Model Development ◽

Housing Demand ◽

Quality Data ◽

Building Stock ◽

Test Arena ◽

Climate Targets ◽

Wide Range ◽

Key Variables ◽

The Impact

It is widely agreed that dynamics of building stocks are relatively poorly known even if it is recognized to be an important research topic. Better understanding of building stock dynamics and future development is crucial, e.g., for sustainable management of the built environment as various analyses require long-term projections of building stock development. Recognizing the uncertainty in relation to long-term modeling, we propose a transparent calculation-based QuantiSTOCK model for modeling building stock development. Our approach not only provides a tangible tool for understanding development when selected assumptions are valid but also, most importantly, allows for studying the sensitivity of results to alternative developments of the key variables. Therefore, this relatively simple modeling approach provides fruitful grounds for understanding the impact of different key variables, which is needed to facilitate meaningful debate on different housing, land use, and environment-related policies. The QuantiSTOCK model may be extended in numerous ways and lays the groundwork for modeling the future developments of building stocks. The presented model may be used in a wide range of analyses ranging from assessing housing demand at the regional level to providing input for defining sustainable pathways towards climate targets. Due to the availability of high-quality data, the Finnish building stock provided a great test arena for the model development.

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Evaluation of statistical methods for quantifying fractal scaling in water-quality time series with irregular sampling

Hydrology and Earth System Sciences ◽

10.5194/hess-22-1175-2018 ◽

2018 ◽

Vol 22 (2) ◽

pp. 1175-1192 ◽

Cited By ~ 2

Author(s):

Qian Zhang ◽

Ciaran J. Harman ◽

James W. Kirchner

Keyword(s):

Water Quality ◽

Time Series ◽

Irregular Sampling ◽

Quality Data ◽

Sampled Data ◽

Spectral Slope ◽

Water Quality Data ◽

Fractal Scaling ◽

Wide Range ◽

Irregularly Sampled Data

Abstract. River water-quality time series often exhibit fractal scaling, which here refers to autocorrelation that decays as a power law over some range of scales. Fractal scaling presents challenges to the identification of deterministic trends because (1) fractal scaling has the potential to lead to false inference about the statistical significance of trends and (2) the abundance of irregularly spaced data in water-quality monitoring networks complicates efforts to quantify fractal scaling. Traditional methods for estimating fractal scaling – in the form of spectral slope (β) or other equivalent scaling parameters (e.g., Hurst exponent) – are generally inapplicable to irregularly sampled data. Here we consider two types of estimation approaches for irregularly sampled data and evaluate their performance using synthetic time series. These time series were generated such that (1) they exhibit a wide range of prescribed fractal scaling behaviors, ranging from white noise (β  =  0) to Brown noise (β  =  2) and (2) their sampling gap intervals mimic the sampling irregularity (as quantified by both the skewness and mean of gap-interval lengths) in real water-quality data. The results suggest that none of the existing methods fully account for the effects of sampling irregularity on β estimation. First, the results illustrate the danger of using interpolation for gap filling when examining autocorrelation, as the interpolation methods consistently underestimate or overestimate β under a wide range of prescribed β values and gap distributions. Second, the widely used Lomb–Scargle spectral method also consistently underestimates β. A previously published modified form, using only the lowest 5 % of the frequencies for spectral slope estimation, has very poor precision, although the overall bias is small. Third, a recent wavelet-based method, coupled with an aliasing filter, generally has the smallest bias and root-mean-squared error among all methods for a wide range of prescribed β values and gap distributions. The aliasing method, however, does not itself account for sampling irregularity, and this introduces some bias in the result. Nonetheless, the wavelet method is recommended for estimating β in irregular time series until improved methods are developed. Finally, all methods' performances depend strongly on the sampling irregularity, highlighting that the accuracy and precision of each method are data specific. Accurately quantifying the strength of fractal scaling in irregular water-quality time series remains an unresolved challenge for the hydrologic community and for other disciplines that must grapple with irregular sampling.

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