Temporal variability in quantitative human gut microbiome profiles and implications for clinical research

AbstractWhile clinical gut microbiota research is ever-expanding, extending reference knowledge of healthy between- and within-subject gut microbiota variation and its drivers remains essential; in particular, temporal variability is under-explored, and a comparison with cross-sectional variation is missing. Here, we perform daily quantitative microbiome profiling on 713 fecal samples from 20 Belgian women over six weeks, combined with extensive anthropometric measurements, blood panels, dietary data, and stool characteristics. We show substantial temporal variation for most major gut genera; we find that for 78% of microbial genera, day-to-day absolute abundance variation is substantially larger within than between individuals, with up to 100-fold shifts over the study period. Diversity, and especially evenness indicators also fluctuate substantially. Relative abundance profiles show similar but less pronounced temporal variation. Stool moisture, and to a lesser extent diet, are the only significant host covariates of temporal microbiota variation, while menstrual cycle parameters did not show significant effects. We find that the dysbiotic Bact2 enterotype shows increased between- and within-subject compositional variability. Our results suggest that to increase diagnostic as well as target discovery power, studies could adopt a repeated measurement design and/or focus analysis on community-wide microbiome descriptors and indices.

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Gut Microbiota Profile and Its Association with Clinical Variables and Dietary Intake in Overweight/Obese and Lean Subjects: A Cross-Sectional Study

Nutrients ◽

10.3390/nu13062032 ◽

2021 ◽

Vol 13 (6) ◽

pp. 2032

Author(s):

Judit Companys ◽

Maria José Gosalbes ◽

Laura Pla-Pagà ◽

Lorena Calderón-Pérez ◽

Elisabet Llauradó ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Intake ◽

Saturated Fatty Acids ◽

Cross Sectional Study ◽

Sectional Study ◽

Anthropometric Parameters ◽

Cross Sectional ◽

Negatively Associated ◽

Clinical Variables ◽

Obese Subjects

We aimed to differentiate gut microbiota composition of overweight/obese and lean subjects and to determine its association with clinical variables and dietary intake. A cross-sectional study was performed with 96 overweight/obese subjects and 32 lean subjects. Anthropometric parameters were positively associated with Collinsella aerofaciens, Dorea formicigenerans and Dorea longicatena, which had higher abundance the overweight/obese subjects. Moreover, different genera of Lachnospiraceae were negatively associated with body fat, LDL and total cholesterol. Saturated fatty acids (SFAs) were negatively associated with the genus Intestinimonas, a biomarker of the overweight/obese group, whereas SFAs were positively associated with Roseburia, a biomarker for the lean group. In conclusion, Dorea formicigenerans, Dorea longicatena and Collinsella aerofaciens could be considered obesity biomarkers, Lachnospiraceae is associated with lipid cardiovascular risk factors. SFAs exhibited opposite association profiles with butyrate-producing bacteria depending on the BMI. Thus, the relationship between diet and microbiota opens new tools for the management of obesity.

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Sex differences in the phylum‐level human gut microbiota composition

BMC Microbiology ◽

10.1186/s12866-021-02198-y ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexander Koliada ◽

Vladislav Moseiko ◽

Mariana Romanenko ◽

Oleh Lushchak ◽

Nadiia Kryzhanovska ◽

...

Keyword(s):

Sex Differences ◽

Gut Microbiota ◽

Age Groups ◽

Microbiota Composition ◽

Human Gut ◽

Cross Sectional ◽

Total N ◽

Human Gut Microbiota ◽

Gut Microbiota Composition

Abstract Background Evidence was previously provided for sex-related differences in the human gut microbiota composition, and sex-specific discrepancy in hormonal profiles was proposed as a main determinant of these differences. On the basis of these findings, the assumption was made on the role of microbiota in the sexual dimorphism of human diseases. To date, sex differences in fecal microbiota were demonstrated primarily at lower taxonomic levels, whereas phylum-level differences between sexes were reported in few studies only. In the present population-based cross-sectional research, sex differences in the phylum-level human gut microbiota composition were identified in a large (total n = 2301) sample of relatively healthy individuals from Ukraine. Results Relative abundances of Firmicutes and Actinobacteria, as determined by qRT-PCR, were found to be significantly increased, while that of Bacteroidetes was significantly decreased in females compared to males. The Firmicutes to Bacteroidetes (F/B) ratio was significantly increased in females compared to males. Females had 31 % higher odds of having F/B ratio more than 1 than males. This trend was evident in all age groups. The difference between sexes was even more pronounced in the elder individuals (50+): in this age group, female participants had 56 % higher odds of having F/B ratio > 1 than the male ones. Conclusions In conclusion, sex-specific differences in the phylum-level intestinal microbiota composition were observed in the Ukraine population. The F/B ratio was significantly increased in females compared to males. Further investigation is needed to draw strong conclusions regarding the mechanistic basis for sex-specific differences in the gut microbiota composition and regarding the role of these differences in the initiation and progression of human chronic diseases.

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Lifestyle modifications result in alterations in the gut microbiota in obese children

BMC Microbiology ◽

10.1186/s12866-020-02002-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ky Young Cho

Keyword(s):

Gut Microbiota ◽

Normal Weight ◽

Rrna Gene ◽

Weight Changes ◽

Obese Children ◽

Lifestyle Modifications ◽

Cross Sectional ◽

Fat Loss ◽

Link Type ◽

Firmicutes Phylum

Abstract Background The association between the gut microbiota and pediatric obesity was analyzed in a cross-sectional study. A prospective study of obese children was conducted to assess the gut microbial alterations after a weight change. We collected fecal samples from obese children before and after a 2-month weight reduction program that consisted of individual counseling for nutritional education and physical activity, and we performed 16S rRNA gene amplicon sequencing using an Illumina MiSeq platform. Results Thirty-six participants, aged 7 to 18 years, were classified into the fat loss (n = 17) and the fat gain (n = 19) groups according to the change in total body fat (%) after the intervention. The baseline analysis of the gut microbiota in the preintervention stages showed dysbiotic features of both groups compared with those of normal-weight children. In the fat loss group, significantly decreased proportions of Bacteroidetes phylum, Bacteroidia class, Bacteroidales order, Bacteroidaceae family, and Bacteroides genus, along with increased proportions of Firmicutes phylum, Clostridia class, and Clostridiales order, were observed after intervention. The microbial richness was significantly reduced, without a change in beta diversity in the fat loss group. The fat gain group showed significantly deceased proportions of Firmicutes phylum, Clostridia class, Clostridiales order, Lachnospiraceae family, and Eubacterium hallii group genus, without a change in diversity after the intervention. According to the functional metabolic analysis by the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, the “Nitrate Reduction VI” and “Aspartate Superpathway” pathways were predicted to increase significantly in the fat loss group. The cooccurring networks of genera were constructed and showed the different microbes that drove the changes between the pre- and postintervention stages in the fat loss and fat gain groups. Conclusions This study demonstrated that lifestyle modifications can impact the composition, richness, and predicted functional profiles of the gut microbiota in obese children after weight changes. Trial registration ClinicalTrials.govNCT03812497, registration date January 23, 2019, retrospectively registered.

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Trimethylamine N-Oxide, a Gut Microbiota-Derived Metabolite, Is Associated with Cardiovascular Risk in Psoriasis: A Cross-Sectional Pilot Study

Dermatology and Therapy ◽

10.1007/s13555-021-00547-3 ◽

2021 ◽

Author(s):

Mariusz Sikora ◽

Norbert Kiss ◽

Albert Stec ◽

Joanna Giebultowicz ◽

Emilia Samborowska ◽

...

Keyword(s):

Cardiovascular Risk ◽

Pilot Study ◽

Gut Microbiota ◽

Cross Sectional

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Soy and Frequent Dairy Consumption with Subsequent Equol Production Reveals Decreased Gut Health in a Cohort of Healthy Puerto Rican Women

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18168254 ◽

2021 ◽

Vol 18 (16) ◽

pp. 8254

Author(s):

Mercedes Y. Lacourt-Ventura ◽

Brayan Vilanova-Cuevas ◽

Delmarie Rivera-Rodríguez ◽

Raysa Rosario-Acevedo ◽

Christine Miranda ◽

...

Keyword(s):

Gut Microbiota ◽

Puerto Rican ◽

Soy Isoflavones ◽

Gut Health ◽

Cross Sectional ◽

Female Population ◽

Puerto Rican Women ◽

Dairy Consumption ◽

Incidence And Mortality ◽

Next Generation Sequencing Ngs

The U.S. Hispanic female population has one of the highest breast cancer (BC) incidence and mortality rates, while BC is the leading cause of cancer death in Puerto Rican women. Certain foods may predispose to carcinogenesis. Our previous studies indicate that consuming combined soy isoflavones (genistein, daidzein, and glycitein) promotes tumor metastasis possibly through increased protein synthesis activated by equol, a secondary dietary metabolite. Equol is a bacterial metabolite produced in about 20–60% of the population that harbor and exhibit specific gut microbiota capable of producing it from daidzein. The aim of the current study was to investigate the prevalence of equol production in Puerto Rican women and identify the equol producing microbiota in this understudied population. Herein, we conducted a cross-sectional characterization of equol production in a clinically based sample of eighty healthy 25–50 year old Puerto Rican women. Urine samples were collected and evaluated by GCMS for the presence of soy isoflavones and metabolites to determine the ratio of equol producers to equol non-producers. Furthermore, fecal samples were collected for gut microbiota characterization on a subset of women using next generation sequencing (NGS). We report that 25% of the participants were classified as equol producers. Importantly, the gut microbiota from equol non-producers demonstrated a higher diversity. Our results suggest that healthy women with soy and high dairy consumption with subsequent equol production may result in gut dysbiosis by having reduced quantities (diversity) of healthy bacterial biomarkers, which might be associated to increased diseased outcomes (e.g., cancer, and other diseases).

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Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components

Journal of Personalized Medicine ◽

10.3390/jpm11010035 ◽

2021 ◽

Vol 11 (1) ◽

pp. 35

Author(s):

Zahra A. Barandouzi ◽

Joochul Lee ◽

Kendra Maas ◽

Angela R. Starkweather ◽

Xiaomei S. Cong

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Alpha Diversity ◽

Diversity Indices ◽

Cross Sectional Study ◽

Caffeine Intake ◽

Caffeine Consumption ◽

Cross Sectional ◽

Food Components ◽

Irritable Bowel

The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.

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The associations of gut microbiota and fecal short-chain fatty acids with bone mass were largely mediated by weight status: a cross-sectional study

European Journal of Nutrition ◽

10.1007/s00394-021-02597-x ◽

2021 ◽

Author(s):

Fengyan Chen ◽

Qinzhi Wei ◽

Dafeng Xu ◽

Yuanhuan Wei ◽

Jue Wang ◽

...

Keyword(s):

Fatty Acids ◽

Gut Microbiota ◽

Bone Mass ◽

Weight Status ◽

Short Chain Fatty Acids ◽

Cross Sectional Study ◽

Short Chain ◽

Sectional Study ◽

Cross Sectional ◽

Chain Fatty Acids

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The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young

mSphere ◽

10.1128/msphere.00327-17 ◽

2017 ◽

Vol 2 (5) ◽

Cited By ~ 65

Author(s):

Gaorui Bian ◽

Gregory B. Gloor ◽

Aihua Gong ◽

Changsheng Jia ◽

Wei Zhang ◽

...

Keyword(s):

Data Analysis ◽

Gut Microbiota ◽

Large Scale ◽

Compositional Data ◽

Healthy Lifestyle ◽

Compositional Data Analysis ◽

Surprising Result ◽

Microbiota Composition ◽

Cross Sectional ◽

Age Cohorts

ABSTRACT We report the large-scale use of compositional data analysis to establish a baseline microbiota composition in an extremely healthy cohort of the Chinese population. This baseline will serve for comparison for future cohorts with chronic or acute disease. In addition to the expected difference in the microbiota of children and adults, we found that the microbiota of the elderly in this population was similar in almost all respects to that of healthy people in the same population who are scores of years younger. We speculate that this similarity is a consequence of an active healthy lifestyle and diet, although cause and effect cannot be ascribed in this (or any other) cross-sectional design. One surprising result was that the gut microbiota of persons in their 20s was distinct from those of other age cohorts, and this result was replicated, suggesting that it is a reproducible finding and distinct from those of other populations. The microbiota of the aged is variously described as being more or less diverse than that of younger cohorts, but the comparison groups used and the definitions of the aged population differ between experiments. The differences are often described by null hypothesis statistical tests, which are notoriously irreproducible when dealing with large multivariate samples. We collected and examined the gut microbiota of a cross-sectional cohort of more than 1,000 very healthy Chinese individuals who spanned ages from 3 to over 100 years. The analysis of 16S rRNA gene sequencing results used a compositional data analysis paradigm coupled with measures of effect size, where ordination, differential abundance, and correlation can be explored and analyzed in a unified and reproducible framework. Our analysis showed several surprising results compared to other cohorts. First, the overall microbiota composition of the healthy aged group was similar to that of people decades younger. Second, the major differences between groups in the gut microbiota profiles were found before age 20. Third, the gut microbiota differed little between individuals from the ages of 30 to >100. Fourth, the gut microbiota of males appeared to be more variable than that of females. Taken together, the present findings suggest that the microbiota of the healthy aged in this cross-sectional study differ little from that of the healthy young in the same population, although the minor variations that do exist depend upon the comparison cohort. IMPORTANCE We report the large-scale use of compositional data analysis to establish a baseline microbiota composition in an extremely healthy cohort of the Chinese population. This baseline will serve for comparison for future cohorts with chronic or acute disease. In addition to the expected difference in the microbiota of children and adults, we found that the microbiota of the elderly in this population was similar in almost all respects to that of healthy people in the same population who are scores of years younger. We speculate that this similarity is a consequence of an active healthy lifestyle and diet, although cause and effect cannot be ascribed in this (or any other) cross-sectional design. One surprising result was that the gut microbiota of persons in their 20s was distinct from those of other age cohorts, and this result was replicated, suggesting that it is a reproducible finding and distinct from those of other populations.

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