***TASK*** the task is to summarize an input biomedical literature in six sentences 
    ***INPUT*** the input is a biomedical literature 
    ***OUTPUT*** the output is the summary of an input biomedical literature in six sentences 
    ***DOCUMENTATION*** 
    ***EXAMPLES*** 
    Input: Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut , but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change . Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression . The animal-based diet increased the abundance of bile-tolerant microorganisms ( Alistipes , Bilophila and Bacteroides ) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides ( Roseburia , Eubacterium rectale and Ruminococcus bromii ) . Microbial activity mirrored differences between herbivorous and carnivorous mammals , reflecting trade-offs between carbohydrate and protein fermentation . Foodborne microbes from both diets transiently colonized the gut , including bacteria , fungi and even viruses . Finally , increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat , bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease . In concert , these results demonstrate that the gut microbiome can rapidly respond to altered diet , potentially facilitating the diversity of human dietary lifestyles ABSTRACT We recently demonstrated that cow 's milk fermented with the probiotic Lactobacillus paracasei CBA L74 ( FM-CBAL74 ) reduces the incidence of respiratory and gastrointestinal tract infections in young children attending school . This effect apparently derives from a complex regulation of non-immune and immune protective mechanisms . We investigated whether FM-CBAL74 could regulate gut microbiota composition and butyrate production . We r and omly selected 20 healthy children ( 12 to 48 months ) from the previous r and omized controlled trial , before ( t0 ) and after 3 months ( t3 ) of dietary treatment with FM-CBAL74 ( FM ) or placebo ( PL ) .  Fecal microbiota was profiled using 16S rRNA gene amplicon sequencing , and the fecal butyrate concentration was also measured . Microbial alpha and beta diversities were not significantly different between groups prior to treatment . FM-CBAL74 but not PL treatment increased the relative abundance of Lactobacillus . Individual Blautia , Roseburia , and Faecalibacterium oligotypes were associated with FM-CBAL74 treatment and demonstrated correlative associations with immune biomarkers . Accordingly , PICRUSt analysis predicted an increase in the proportion of genes involved in butyrate production pathways , consistent with an increase in fecal butyrate observed only in the FM group . Dietary supplementation with FM-CBAL74 induces specific signatures in gut microbiota composition and stimulates butyrate production . These effects are associated with changes in innate and acquired immunity . IMPORTANCE The use of a fermented milk product containing the heat-killed probiotic strain Lactobacillus paracasei CBAL74 induces changes in the gut microbiota , promoting the development of butyrate producers . These changes in the gut microbiota composition correlate with increased levels of innate and acquired immunity biomarkers The colonization process of the infant gut microbiome has been called chaotic , but this view could reflect insufficient documentation of the factors affecting the microbiome . We performed a 2.5-y case study of the assembly of the human infant gut microbiome , to relate life events to microbiome composition and function . Sixty fecal sample s were collected from a healthy infant along with a diary of diet and health status . Analysis of > 300,000 16S rRNA genes indicated that the phylogenetic diversity of the microbiome increased gradually over time and that changes in community composition conformed to a smooth temporal gradient . In contrast , major taxonomic groups showed abrupt shifts in abundance corresponding to changes in diet or health . Community assembly was nonr and om : we observed discrete steps of bacterial succession punctuated by life events . Furthermore , analysis of ≈500,000 DNA metagenomic reads from 12 fecal sample s revealed that the earliest microbiome was enriched in genes facilitating lactate utilization , and that functional genes involved in plant polysaccharide metabolism were present before the introduction of solid food , priming the infant gut for an adult diet . However , ingestion of table foods caused a sustained increase in the abundance of Bacteroidetes , elevated fecal short chain fatty acid levels , enrichment of genes associated with carbohydrate utilization , vitamin bio synthesis , and xenobiotic degradation , and a more stable community composition , all of which are characteristic of the adult microbiome . This study revealed that seemingly chaotic shifts in the microbiome are associated with life events ; however , additional experiments ought to be conducted to assess how different infants respond to similar life events BACKGROUND & AIMS It might be possible to manipulate the intestinal microbiota with prebiotics or other agents to prevent or treat obesity . However , little is known about the ability of prebiotics to specifically modify gut microbiota in children with overweight/obesity or reduce body weight . We performed a r and omized controlled trial to study the effects of prebiotics on body composition , markers of inflammation , bile acids in fecal sample s , and composition of the intestinal microbiota in children with overweight or obesity . METHODS We performed a single-center , double-blind , placebo-controlled trial of 2 separate cohorts ( March 2014 and August 2014 ) at the University of Calgary in Canada . Participants included children , 7 - 12 years old , with overweight or obesity ( > 85th percentile of body mass index ) but otherwise healthy . Participants were r and omly assigned to groups given either oligofructose-enriched inulin ( OI ; 8 g/day ; n=22 ) or maltodextrin placebo ( isocaloric dose , controls ; n=20 ) once daily for 16 weeks . Fat mass and lean mass were measured using dual-energy-x-ray absorptiometry . Height , weight , and waist circumference were measured at baseline and every 4 weeks thereafter . Blood sample s were collected at baseline and 16 weeks , and analyzed for lipids , cytokines , lipopolysaccharide , and insulin . Fecal sample s were collected at baseline and 16 weeks ; bile acids were profiled using high-performance liquid chromatography and the composition of the microbiota was analyzed by 16S rRNA sequencing and quantitative polymerase chain reaction . The primary outcome was change in percent body fat from baseline to 16 weeks . RESULTS After 16 weeks , children who consumed OI had significant decreases in body weight z-score ( decrease of 3.1 % ) , percent body fat ( decrease of 2.4 % ) , and percent trunk fat ( decrease of 3.8 % ) compared with children given placebo ( increase of 0.5 % , increase of 0.05 % , and decrease of 0.3 % , respectively ) . Children who consumed OI also had a significant reduction in level of interleukin 6 from baseline ( decrease of 15 % ) compared with the placebo group ( increase of 25 % ) . There was a significant decrease in serum triglycerides ( decrease of 19 % ) in the OI group . Quantitative polymerase chain reaction showed a significant increase in Bifidobacterium spp . in the OI group compared with controls . 16S rRNA sequencing revealed significant increases in species of the genus Bifidobacterium and decreases in Bacteroides vulgatus within the group who consumed OI . In fecal sample s , levels of primary bile acids increased in the placebo group but not in the OI group over the 16-week study period . CONCLUSIONS In a placebo-controlled , r and omized trial , we found a prebiotic ( OI ) to selectively alter the intestinal microbiota and significantly reduce body weight z-score , percent body fat , percent trunk fat , and serum level of interleukin 6 in children with overweight or obesity ( Clinical trials.gov no : NCT02125955 ) Importance Establishment of the infant microbiome has lifelong implication s on health and immunity . Gut microbiota of breastfed compared with nonbreastfed individuals differ during infancy as well as into adulthood . Breast milk contains a diverse population of bacteria , but little is known about the vertical transfer of bacteria from mother to infant by breastfeeding . Objective To determine the association between the maternal breast milk and areolar skin and infant gut bacterial communities . Design , Setting , and Participants In a prospect i ve , longitudinal study , bacterial composition was identified with sequencing of the 16S ribosomal RNA gene in breast milk , areolar skin , and infant stool sample s of 107 healthy mother-infant pairs . The study was conducted in Los Angeles , California , and St Petersburg , Florida , between January 1 , 2010 , and February 28 , 2015 . Exposures Amount and duration of daily breastfeeding and timing of solid food introduction . Main Outcomes and Measures Bacterial composition in maternal breast milk , areolar skin , and infant stool by sequencing of the 16S ribosomal RNA gene . Results In the 107 healthy mother and infant pairs ( median age at the time of specimen collection , 40 days ; range , 1 - 331 days ) , 52 ( 43.0 % ) of the infants were male .  Bacterial communities were distinct in milk , areolar skin , and stool , differing in both composition and diversity . The infant gut microbial communities were more closely related to an infant ’s mother ’s milk and skin compared with a r and om mother ( mean difference in Bray-Curtis distances , 0.012 and 0.014 , respectively ; P < .001 for both ) . Source tracking analysis was used to estimate the contribution of the breast milk and areolar skin microbiomes to the infant gut microbiome . During the first 30 days of life , infants who breastfed to obtain 75 % or more of their daily milk intake received a mean ( SD ) of 27.7 % ( 15.2 % ) of the bacteria from breast milk and 10.3 % ( 6.0 % ) from areolar skin . Bacterial diversity ( Faith phylogenetic diversity , P = .003 ) and composition changes were associated with the proportion of daily breast milk intake in a dose-dependent manner , even after the introduction of solid foods . Conclusions and Relevance The results of this study indicate that bacteria in mother ’s breast milk seed the infant gut , underscoring the importance of breastfeeding in the development of the infant gut microbiome The potential influence of maternal obesity on infant gut microbiota may occur either through vertically transmitted microbes or through the dietary habits of the family . Recent studies have suggested that the heritability of obesity may partly be caused by the transmission of “ obesogenic ” gut microbes . However , the findings presented here suggest that maternal obesity per se does not affect the overall composition of the gut microbiota and its development after introduction of complementary foods . Rather , progression in complementary feeding is found to be the major determinant for gut microbiota establishment . Exp and ing our underst and ing of the influence of complementary diet on the development and establishment of the gut microbiota will provide us with the knowledge to tailor a beneficial progression of our intestinal microbial community . ABSTRACT The first years of life are paramount in establishing our endogenous gut microbiota , which is strongly affected by diet and has repeatedly been linked with obesity . However , very few studies have addressed the influence of maternal obesity on infant gut microbiota  , which may occur either through vertically transmitted microbes or through the dietary habits of the family . Additionally , very little is known about the effect of diet during the complementary feeding period , which is potentially important for gut microbiota development . Here , the  gut microbiotas  of two different cohorts of infants , born either of a r and om sample of healthy mothers ( n = 114 ) , or of obese mothers ( n = 113 ) , were profiled by 16S rRNA amplicon sequencing . Gut microbiota data were compared to breastfeeding patterns and detailed individual dietary recordings to assess effects of the complementary diet . We found that  maternal obesity  did not influence microbial diversity or specific taxon abundances during the complementary feeding period . Across cohorts , breastfeeding duration and composition of the complementary diet were found to be the major determinants of gut microbiota development . In both cohorts , gut microbial composition and alpha diversity were thus strongly affected by introduction of family foods with high protein and fiber contents . Specifically , intake of meats , cheeses , and Danish rye bread , rich in protein and fiber , were associated with increased alpha diversity . Our results reveal that the transition from early infant feeding to family foods is a major determinant for gut microbiota development . IMPORTANCE The potential influence of maternal obesity on infant gut microbiota may occur either through vertically transmitted microbes or through the dietary habits of the family . Recent studies have suggested that the heritability of obesity may partly be caused by the transmission of “ obesogenic ” gut microbes . However , the findings presented here suggest that maternal obesity per se does not affect the overall composition of the gut microbiota and its development after introduction of complementary foods . Rather , progression in complementary feeding is found to be the major determinant for gut microbiota establishment . Exp and ing our underst and ing of the influence of complementary diet on the development and establishment of the gut microbiota will provide us with the knowledge to tailor a beneficial progression of our intestinal microbial community The gut of the human neonate is colonized rapidly after birth from an early sparse and highly distinct microbiota to a more adult-like and convergent state , within  
    Output:
    
Geographic location and 16S rRNA sequencing region were independently associated with microbial proportions .