Differences In Fecal Microbiota Composition Research Articles

Metabolic and inflammatory profiles, gut microbiota and lifestyle factors in overweight and normal weight young thai adults.

Obesity among young adults, especially those living in developing countries is increasing. A high body mass index (BMI) is one of the major causes of several diseases worldwide, constituting an important risk factor for non-communicable diseases (NCDs). Investigations describing the relationship between BMI, clinical and gut microbiota characteristics and lifestyle factors of overweight young adults, especially from Southeast Asian countries are limited. Metabolic and inflammatory biomarkers, fecal microbiota profiles and lifestyle factors were compared between overweight Thai young adults (n = 30, mean age 33 ± 9.48) and those with normal weight (n = 30, mean age 27 ±7.50). This study was registered with the Thai Clinical Trials Registry (TCTR20220204007). Health status including body composition, fasting glucose and insulin, lipid profiles, liver and kidney function, inflammatory biomarkers, blood pressure and fecal microbiota using 16S rRNA gene sequencing data was determined. Dietary intake was assessed using a 3-day dietary record and a food frequency questionnaire (FFQ), with physical activity levels compared using the international physical activity questionnaire (IPAQ). The overweight group had significantly higher BMI, waist-hip ratio, body fat mass, % body fat, skeletal mass, triglyceride level, C-reactive protein, insulin and blood pressure, with lower levels of high-density lipoprotein cholesterol (HDL-C) and blood urea nitrogen compared to the normal weight group. Significant differences in fecal microbiota composition at the family and genus levels were observed between the two groups. In our clinical setting, we also observed that unhealthy diets with high consumption of food rich in fat and sugar, processed meat and alcohol, and physical inactivity were associated with an increased prevalence of overweight in Thai young adults. Results provided the big picture of health and lifestyle characteristics of overweight young Thai people. Young adults should be encouraged to engage in health-promoting activities that maintain healthy bodyweight.

Diet Quality and the Fecal Microbiota in Adults in the American Gut Project

BackgroundThe Dietary Guidelines for Americans advises on dietary intake to meet nutritional needs, promote health, and prevent diseases. Diet affects the intestinal microbiota and is increasingly linked to health. It is vital to investigate the relationships between diet quality and the microbiota to better understand the impact of nutrition on human health. ObjectivesThis study aimed to investigate the differences in fecal microbiota composition in adults from the American Gut Project based on their adherence to the Dietary Guidelines for Americans. MethodsThis study was a cross-sectional analysis of the 16S sequencing and food frequency data of a subset of adults (n = 432; age = 18–60 y; 65% female, 89% white) participating in the crowdsourced American Gut Project. The Healthy Eating Index-2015 assessed the compliance with Dietary Guideline recommendations. The cohort was divided into tertiles based on Healthy Eating Index-2015 scores, and differences in taxonomic abundances and diversity were compared between high and low scorers. ResultsThe mean Total Score for low-scoring adults (58.1 ± 5.4) was comparable with the reported score of the average American adult (56.7). High scorers for the Total Score and components related to vegetables, grains, and dairy had greater alpha diversity than low scorers. High scorers in the fatty acid component had a lower alpha diversity than low scorers (95% CI: 0.35, 1.85). A positive log-fold difference in abundance of plant carbohydrate–metabolizing taxa in the families Lachnospiraceae and Ruminococcaceae was observed in high-scoring tertiles for Total Score, vegetable, fruit, and grain components (Benjamini–Hochberg; q < 0.05). ConclusionsAdults with greater compliance to the Dietary Guidelines demonstrated higher diversity in their fecal microbiota and greater abundance of bacteria capable of metabolizing complex carbohydrates, providing evidence on how Dietary Guidelines support the gut microbiota.

Associations between Accelerometer-Measured Physical Activity and Fecal Microbiota in Adults with Overweight and Obesity.

We aimed to assess whether total daily physical activity (PA), PA intensities, sedentary time (ST), and prolonged ST are associated with differences in the gut microbiota composition or short-chain fatty acid (SCFA) profile of adults with overweight or obesity. Cross-sectional associations between total daily PA (counts per minute), PA intensities (light and moderate-to-vigorous (MVPA)), ST, prolonged ST, and fecal microbiota composition were assessed in adults ( n = 124) between 25 and 45 yr of age with body mass index ≥25 kg·m -2 . Fecal microbiota composition was assessed with 16S rRNA gene sequencing. Daily PA and ST were measured with a hip-worn ActiGraph wGT3X-BT accelerometer. Daily PA volume and intensity were positively associated with relative abundance of Faecalibacterium ( P = 0.04) and negatively associated with the abundances of Alistipes , Parabacteroides , and Gemmiger ( P = 0.003-0.04) as well as the concentrations of acetate, butyrate, and total SCFA (all P = 0.04). Conversely, ST was negatively associated with abundance of Faecalibacterium but positively associated with the abundances of taxa, including Ruminococcaceae, Parabacteroides , Alistipes , and Gemmiger . Clustering of participants based on whether they met PA recommendations suggested that SCFA profiles differed between individuals who did and did not meet PA recommendations. K-means clustering based on percent of time spent in MVPA and ST also identified differences in fecal microbiota composition between cluster 1 (lower MVPA, higher ST) and cluster 2 (higher MVPA, lower ST), including a higher abundance of Alistipes in cluster 1. The current analysis suggests a beneficial association of daily PA on the fecal microbiota and a negative association of ST, particularly with respect to the associations of these variables with the genera Faecalibacterium , a butyrate-producing taxon.

Microbiota of vaccinated and non-vaccinated clinically inconspicuous and conspicuous piglets under natural Lawsonia intracellularis infection.

Lawsonia (L.) intracellularis is a widespread, economically important bacterium causing the porcine proliferative enteropathy (PPE). In this study, we evaluated intestinal microbiota of naturally exposed L. intracellularis-positive pigs under standardized conditions. To obtain three independent repetitions, 27 L. intracellularis-infected pigs (19.0 ± 1.50 kg body weight) from one farm were divided into three groups at an age of 7 to 8 weeks (nine pigs/group). Pigs were either vaccinated against L. intracellularis via oral drenching on their 21st day of life (attenuated live vaccine) or non-vaccinated and selected according to clinical findings (pigs without deviating fecal consistency or with moderate to soft fecal consistency). Comparison of the clinically inconspicuous piglets that differed regarding their vaccination status showed fewer significant differences in fecal microbiota composition. The vaccination led to an overall enrichment of bacterial species belonging to the order Clostridiales, while species of the genus Collinsella and Prevotella were decreased. Several bacterial species belonging to the order Bacteroidales, mainly of the family Prevotellacecae, often closely matching Prevotella copri differed significantly between non-vaccinated clinically inconspicuous and conspicuous piglets. Whether those bacterial species play a role in mitigating the severity of an L. intracellularis infection remains to be defined.

Analysis of the developing gut microbiota in young dairy calves\u2014impact of colostrum microbiota and gut disturbances

The aim of this study was to characterize the colostrum and fecal microbiota in calves and to investigate whether fecal microbiota composition was related to colostrum microbiota or factors associated with calf health. Colostrum samples were collected in buckets after hand milking of 76 calving cows from 38 smallholder dairy farms. Fecal samples were taken directly from the rectum of 76 calves at birth and at 14 days age. The bacterial community structure in colostrum and feces was analyzed by terminal restriction fragment length polymorphism for all samples, and the microbial composition was determined by 16S rRNA gene amplicon sequencing for a subset of the samples (8 colostrum, 40 fecal samples). There was a significant difference in fecal microbiota composition between day 0 and day 14 samples, but no associations between the microbiota and average daily gain, birth weight, or transfer of passive immunity. At 14 days of age, Faecalibacterium and Butyricicoccus were prevalent in higher relative abundances in the gut of healthy calves compared to calves with diarrhea that had been treated with antimicrobials. Colostrum showed great variation in composition of microbiota but no association to fecal microbiota. This study provides the first insights into the composition of colostrum and fecal microbiota of young dairy calves in southern Vietnam and can form the basis for future more detailed studies.

Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn\u2019s disease

BackgroundThe role of the fecal microbiota composition for the postoperative disease course of patients with Crohn’s disease (CD) who have undergone ileocecal resection remains to be established. In this study, we investigated if the fecal microbiota composition, determined by a high throughput test quantifying a pre-selected set of bacteria, is associated with the postoperative disease course of CD patients.MethodsFecal samples were obtained from healthy subjects as well as from CD patients, 3–10 weeks and 1 year after ileocaecal resection. The fecal microbial composition was analyzed by Genetic Analysis GA-map Dysbiosis test, targeting ≥300 bacteria on different taxonomic levels. Postoperative disease status was assessed endoscopically according to Rutgeerts scoring system 1 year after surgery. Differences in fecal microbiota composition between groups were analyzed by multivariate factor analyses and cluster analysis. Microbial stability over time was determined using Bray-Curtis dissimilarity.ResultsOne year after surgery, the fecal microbiota composition differed between CD patients (n = 21) and healthy subjects (n = 7). At this time point, the microbiota composition of CD patients was associated with disease course, clearly separating patients with disease relapse (n = 8) and patients in remission (n = 13). Further, the microbial within-patient stability was high during the first year after surgery, irrespective of disease course.ConclusionThe fecal microbiota composition of CD patients, analyzed by GA-map Dysbiosis test, is subject to little variation over time, and may potentially be used as a non-invasive diagnostic tool for the postoperative disease course.

Late weaning is associated with increased microbial diversity and Faecalibacterium prausnitzii abundance in the fecal microbiota of piglets

BackgroundIn pig production systems, weaning is a crucial period characterized by nutritional, environmental, and social stresses. Piglets transition from a milk-based diet to a solid, more complex plant-based diet, and their gut physiology must adapt accordingly. It is well established that piglets weaned later display improved health, better wean-to-finish growth performance, and lower mortality rates. The aim of this study was to evaluate the impact of weaning age on fecal microbiota diversity and composition in piglets. Forty-eight Large White piglets were divided into 4 groups of 12 animals that were weaned at different ages: 14 days (early weaning), 21 days (a common weaning age in intensive pig farming), 28 days (idem), and 42 days (late weaning). Microbiota composition was assessed in each group by sequencing the 16S rRNA gene using fecal samples taken on the day of weaning, 7 days later, and at 60 days of age.ResultsIn each group, there were significant differences in fecal microbiota composition before and after weaning (p < 0.05), confirming that weaning can drastically change the gut microbiota. Microbiota diversity was positively correlated with weaning age: microbial alpha diversity and richness were higher in piglets weaned at 42 days of age both on the day of weaning and 7 days later. The abundance of Faecalibacterium prausnitzii operational taxonomic units (OTUs) was also higher in piglets weaned at 42 days of age.ConclusionsOverall, these results show that late weaning increased gut microbiota diversity and the abundance of F. prausnitzii, a microorganism with positive effects in humans. Piglets might thus derive a competitive advantage from later weaning because they have more time to accumulate a higher diversity of potentially beneficial microbes prior to the stressful and risky weaning period.

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption

Irritable bowel syndrome (IBS) is a heterogeneous disorder, but diagnoses and determination of subtypes are made based on symptoms. We profiled the fecal microbiomes of patients with and without IBS to identify biomarkers of this disorder. We collected fecal and urine samples from 80 patients with IBS (Rome IV criteria; 16-70 years old) and 65 matched individuals without IBS (control individuals), along with anthropometric, medical, and dietary information. Shotgun and 16S ribosomal RNA amplicon sequencing were performed on feces, whereas urine and fecal metabolites were analyzed by gas chromatography and liquid chromatography-mass spectrometry. Co-occurrence networks were generated based on significant Spearman correlations between data. Bile acid malabsorption (BAM) was identified in patients with diarrhea by retention of radiolabeled selenium-75 homocholic acid taurine. Patients with IBS had significant differences in network connections between diet and fecal microbiomes compared with control individuals; these were accompanied by differences in fecal metabolomes. We did not find significant differences in fecal microbiota composition among patients with different IBS symptom subtypes. Fecal metabolome profiles could discriminate patients with IBS from control individuals. Urine metabolomes also differed significantly between patients with IBS and control individuals, but most discriminatory metabolites were related to diet or medications. Fecal metabolomes, but not microbiomes, could distinguish patients with IBS with vs those without BAM. Despite the heterogeneity of IBS, patients have significant differences in urine and fecal metabolomes and fecal microbiome vs control individuals, independent of symptom-based subtypes of IBS. Fecal metabolome analysis can be used to distinguish patients with IBS with vs those without BAM. These findings might be used for developing microbe-based treatments for these disorders.

Relationship between faecal microbiota and plasma metabolome in rats fed NK603 and MON810 GM maize from the GMO90+ study

Safety concerns arising from the consumption of foods derived from genetically modified (GM) crops remains a controversial subject. We report here a faecal microbiota compositional analysis in Wistar rats from the GMO90 + study, which fed glyphosate-tolerant NK603 (+/− Roundup application) and Bt toxin MON810 GM maize for 6 months in comparison to their closest non-GM isogenic lines. We first integrated the faecal microbiota compositional data with results from plasma metabolomics to understand which bacterial species can influence host metabolism. Coriobacteriaceae and Acetatifactor significantly predicted plasma metabolic profile in males, while Bifidobacterium and Ruminococcus were able to predict female plasma metabolites. We then investigated the differences in fecal microbiota composition between group of rats fed MON810 or NK603 GM maize in comparison to their isogenic lines. Bacterial community richness was not altered by the test diets. There were no statistically significant differences in taxa abundance in the rat faecal microbiota that we could attribute to the consumption of either MON810 or NK603. We show that the consumption of the widely cultivated GM maize varieties NK603 and MON810 even up to 33% of the total diet had no effect on the status of the faecal microbiota compared to non-GM near isogenic lines.

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation

A high prevalence of adherent-invasive E. coli (AIEC) in the intestinal mucosa of Crohn’s disease patients has been shown. AIEC colonize the intestine and induce inflammation in genetically predisposed mouse models including CEABAC10 transgenic (Tg) mice expressing human CEACAM6-receptor for AIEC and eif2ak4−/− mice exhibiting autophagy defect in response to AIEC infection. Here, we aimed at investigating whether gut microbiota modification contributes to AIEC-induced intestinal inflammation in these mouse models. For this, eif2ak4+/+ and eif2ak4−/− mice or CEABAC10 Tg mice invalidated for Eif2ak4 gene (Tg/eif2ak4−/−) or not (Tg/eif2ak4+/+) were infected with the AIEC reference strain LF82 or the non-pathogenic E. coli K12 MG1655 strain. In all mouse groups, LF82 colonized the gut better and longer than MG1655. No difference in fecal microbiota composition was observed in eif2ak4+/+ and eif2ak4−/− mice before infection and at day 1 and 4 post-infection. LF82-infected eif2ak4−/− mice exhibited altered fecal microbiota composition at day 14 and 21 post-infection and increased fecal lipocalin-2 level at day 21 post-infection compared to other groups, indicating that intestinal inflammation developed after microbiota modification. Similar results were obtained for LF82-infected Tg/eif2ak4−/− mice. These results suggest that in genetically predisposed hosts, AIEC colonization might induce chronic intestinal inflammation by altering the gut microbiota composition.

Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity

Objectives: Several studies have reported that the intestinal microbiota composition of celiac disease (CD) patients differs from healthy individuals. The possible role of gut microbiota in the pathogenesis of the disease is, however, not known. Here, we aimed to assess the possible differences in early fecal microbiota composition between children that later developed CD and healthy controls matched for age, sex and HLA risk genotype.Materials and methods: We used 16S rRNA gene sequencing to examine the fecal microbiota of 27 children with high genetic risk of developing CD. Nine of these children developed the disease by the age of 4 years. Stool samples were collected at the age of 9 and 12 months, before any of the children had developed CD. The fecal microbiota composition of children who later developed the disease was compared with the microbiota of the children who did not have CD or associated autoantibodies at the age of 4 years. Delivery mode, early nutrition, and use of antibiotics were taken into account in the analyses.Results: No statistically significant differences in the fecal microbiota composition were found between children who later developed CD (n = 9) and the control children without disease or associated autoantibodies (n = 18).Conclusions: Based on our results, the fecal microbiota composition at the age of 9 and 12 months is not associated with the development of CD. Our results, however, do not exclude the possibility of duodenal microbiota changes or a later microbiota-related trigger for the disease.

Dysbiosis of the fecal microbiota in feedlot cattle with hemorrhagic diarrhea

The bovine gastrointestinal microbiota is a complex polymicrobial ecosystem that plays an important role in maintaining mucosal health. The role of mucosal microbial populations in the pathogenesis of gastrointestinal diseases has been well established in other species. However, limited information is available about changes in the fecal microbiota that occur under disease conditions, such as hemorrhagic diarrhea in feedlot cattle. The objectives of this study were to characterize the differences in fecal microbiota composition, diversity and functional gene profile between feedlot calves with, and without, hemorrhagic diarrhea. Deep fecal swabs were collected from calves with hemorrhagic diarrhea (n = 5) and from pen matched healthy calves (n = 5). Genomic DNA was extracted, and V1-V3 hypervariable region of 16S rRNA gene was amplified and sequenced using the Illumina MiSeq sequencing. When compared to healthy calves, feedlot cattle with hemorrhagic diarrhea showed significant increases in the relative abundance of Clostridium, Blautia and Escherichia, and significant decreases in the relative abundance of Flavobacterium, Oscillospira, Desulfonauticus, Ruminococcus, Thermodesulfovibrio and Butyricimonas. Linear discriminant analysis effect size (LEfSe) also revealed significant differences in bacterial taxa between healthy calves and hemorrhagic diarrhea calves. This apparent dysbiosis in fecal microbiota was associated with significant differences in the predictive functional metagenome profiles of these microbial communities. In summary, our results revealed a bacterial dysbiosis in fecal samples of calves with hemorrhagic diarrhea, with the diseased calves exhibiting less diversity and fewer observed species compared to healthy controls. Additional studies are warranted in a larger cohort of animals to help elucidate the trajectory of change in fecal microbial communities, and their predictive functional capacity, in calves with other gastrointestinal diseases.

Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia

The purpose of this study was to discover differences in the human fecal microbiota composition driven by long-term omnivore versus vegan/lacto-vegetarian dietary pattern. In addition, the possible association of demographic characteristics and dietary habits such as consumption of particular foods with the fecal microbiota was examined. This study was conducted on a Slovenian population comprising 31 vegetarian participants (11 lacto-vegetarians and 20 vegans) and 29 omnivore participants. Bacterial DNA was extracted from the frozen fecal samples by Maxwell 16 Tissue DNA Purification Kit (Promega). Relative quantification of selected bacterial groups was performed by real-time PCR. Differences in fecal microbiota composition were evaluated by PCR-DGGE fingerprinting of the V3 16S rRNA region. Participants' demographic characteristics, dietary habits and health status information were collected through a questionnaire. Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa. Real-time PCR also showed a higher concentration and ratio of Enterobacteriaceae (16S rDNA copies/g and %) in female participants (p<0.05 and p<0.01) and decrease in Bifidobacterium with age (p<0.01). DGGE analysis of the 16S rRNA V3 region showed that relative quantity of DGGE bands from certain bacterial groups was lower (Bifidobacterium, Streptococus, Collinsella and Lachnospiraceae) or higher (Subdoligranulum) among vegetarians, indicating the association of dietary type with bacterial community composition. Sequencing of selected DGGE bands revealed the presence of common representatives of fecal microbiota: Bacteroides, Eubacterium, Faecalibacterium, Ruminococcaceae, Bifidobacterium and Lachnospiraceae. Up to 4% of variance in microbial community analyzed by DGGE could be explained by the vegetarian type of diet. Long-term vegetarian diet contributed to quantity and associated bacterial community shifts in fecal microbiota composition. Consumption of foods of animal origin (eggs, red meat, white meat, milk, yoghurt, other dairy products, fish and seafood) and vegetarian type of diet explained the largest share of variance in microbial community structure. Fecal microbiota composition was also associated with participants' age, gender and body mass.

Effects of a simple or a complex starter microbiota on intestinal microbiota composition in caesarean derived piglets1

The present study was designed to develop a model in piglets that allows the investigation of the effects of postnatal association with a simple or a complex microbiota on gut health and development. Thirty piglets from 2 sows were obtained by caesarean delivery (day 0) and were equally divided over 2 treatment groups housed in separate clean, nonsterile rooms. All piglets received orally a simple microbiota consisting of Lactobacillus amylovorus, Clostridium glycolicum, and Parabacteroides spp. on days 1, 2, and 3 after birth. On day 3 and 4 the piglets received either a complex microbiota by providing them with a fecal inoculant of an adult sow [complex association (CA)] or a placebo inoculant [simple association (SA)]. Fecal microbiota composition, as determined by denaturing gradient gel electrophoresis and by pig intestinal tract chip (PITChip) analysis of 16S rRNA genes (days 3, 5, 7, 14, and 28), was less diverse in the SA group compared to the CA group. A difference in fecal microbiota composition between treatments persisted until the end of the study. It was concluded that the composition of microbiota in feces of cesarean delivery-derived piglets is influenced by bacterial association in the first days after birth. Differences in fecal microbiota composition between piglets exposed to a simple or complex inoculum at early age persisted for at least 3 wk.

Associations between dietary habits and body mass index with gut microbiota composition and fecal water genotoxicity: an observational study in African American and Caucasian American volunteers

BackgroundAfrican Americans (AA) suffer from an increased incidence and mortality of colorectal cancer (CRC). Environmental exposures including dietary habits likely contribute to a high burden of CRC, however, data on the dietary habits of AA is sparse. Diet might change the composition and the activities of the intestinal microbiota, in turn affecting fecal genotoxicity/mutagenicity that is thought to be associated with carcinogenesis.MethodsWe assessed dietary habits by food frequency questionnaire and by food records in 52 AA and 46 CA residents of the Eastern Shore of MD. Fecal microbiota composition was determined using 16S rRNA based methods and fecal genotoxicity measured using the Comet assay.ResultsAA reported an increased intake of heterocyclic amines and a decreased dietary intake of vitamins including vitamin D (p < 0.05) that correlated with differences in fecal microbiota composition but not fecal genotoxicity. Intake of dietary fiber, calcium, total fat and heterocyclic amines correlated with differences in microbiota composition. Total bacterial counts/g of stool and raw counts of Bacteroides were increased in AA. In contrast to a previous study, BMI was not associated with proportions of Bacteroides.ConclusionDietary habits of African Americans, including increased HCA intake and decreased vitamin D intake might at least partially contribute to CRC through modifications of gut microbiota composition that result in changes of the intestinal milieu.

Early differences in fecal microbiota composition in children may predict overweight

Background: Experimental studies suggest that gut microbiota deviations predispose toward energy storage and obesity.Objective: We wanted to establish whether early gut microbiota composition can guide weight development throughout early childhood.Design: Overweight and obese children (n = 25) were selected from a prospective follow-up study at the age of 7 y and identified according to the International Obesity Task Force criteria. Normal-weight children (n = 24) were selected from the same cohort and matched for gestational age and body mass index at birth, mode of delivery, probiotic supplementation, duration of breastfeeding, use of antibiotics during infancy, and frequencies of atopic diseases and atopic sensitization. Early fecal microbiota composition was analyzed by fluorescent in situ hybridization (FISH) with microscopic and flow cytometry detection and by quantitative real-time polymerase chain reaction (qRT-PCR).Results: The bifidobacterial numbers in fecal samples during infancy, as assessed by the FISH with flow cytometry, were higher in children remaining normal weight, [median: 2.19 × 109 cells/g (interquartile range: 1.10–5.28 × 109 cells/g)] than in children becoming overweight [1.20× 109 cells/g (0.48–1.59× 109 cells/g); P = 0.02]. A similar tendency was found by FISH with microscopic detection and qRT-PCR. The microbiota aberrancy during infancy in children becoming overweight was also associated with a greater number of Staphylococcus aureus [0.64 × 106 cells/g (0.33–1.00× 106 cells/g)] than in children remaining normal weight [0.27 × 106 cells/g (0.17–0.50 × 106 cells/g); P = 0.013].Conclusion: Aberrant compositional development of the gut microbiota precedes overweight, offering new possibilities for preventive and therapeutic applications in weight management.

Fecal microbiota in sensitized wheezy and non‐sensitized non‐wheezy children: a nested case–control study

It has been suggested that intestinal microbiota of allergic and non-allergic children differs in composition, and that microbiota-immune system interactions may predispose children to develop sensitization. Previous studies have examined fecal microbiota of allergic children with atopic dermatitis, but little is known about that of atopic wheezy children. To investigate the composition of the fecal microbiota of young sensitized wheezy and non-sensitized non-wheezy children, using molecular methods. Within the context of a prospective birth cohort, we carried out a nested case-control study of sensitized wheezy children (cases) and non-sensitized non-wheezy controls. Cases and controls were matched for age, sex, parental atopy, allergen exposure, and pet ownership. We evaluated the composition of fecal microbiota by nucleic acid-based methods (PCR combined with denaturing gradient gel electrophoresis and quantification of bifidobacteria by fluorescent in situ hybridization). Thirty-three case-control pairs (mean age 4.4 years) provided stool samples. Comparison of total bacterial community profiles showed that each child had a unique fecal microbiota (mean Dice's similarity coefficient 22%, range 3.3-60.8%). There was no difference between the groups in prevalence of Lactic Acid bacteria (12/33 vs. 11/33, P=0.8) or bifidobacteria (30/33 vs. 31/33, P=1.00, cases vs. controls). The bifidobacterial species detected were similar in both groups. The percentage of bifidobacteria in total fecal microflora was no different between cases (median 1.7%, range 0-20.8%) and controls (1.9%, 0-18.2%, P=0.7). However, cases with eczema had significantly fewer bifidobacteria (median 1.6%, range 0-4.8%) than their controls (4.0%, 1.9-18.2%, P=0.05). We found no differences in fecal microbiota composition between sensitized wheezy and non-sensitized, non-wheezy children aged 3-5 years using nucleic acid-based methods. Differences appear to be isolated to those allergic children with eczema.