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Historically, humans have interacted with soils, which contain a rich source of microorganisms. Fruit and vegetable gardening is the primary interaction humans have with soil today. Animal research reveals that soil microorganisms can be transferred to the rodent intestine. However, studies on fecal and soil microbial changes associated with gardening in humans are lacking. The current case-controlled cohort study aimed to characterize the fecal and soil microbiota of gardening families (n = 10) and non-gardening (control) families (n = 9). Families included two adults and one child (5-18 years) for a total of 56 participants. All participants provided a fecal sample, soil sample, and diet history questionnaires before the gardening season (April) and during the peak of the gardening season (August). Healthy Eating Index (HEI-2015) scores and nutrient analysis were performed. Fecal and soil DNA were extracted and amplified. Sequence data were then processed and analyzed. Peak season gardening families tended to have greater fecal operational features, a greater Faith's Phylogenetic Diversity score, greater fiber intake, and higher abundances of fiber fermenting bacteria than peak control families. Soil endemic microbes were also shared with gardening participant's fecal samples. This study revealed that the fecal microbiota of gardening families differs from non-gardening families, and that there are detectable changes in the fecal microbial community of gardeners and their family members over the course of the gardening season. Additional research is necessary to determine if changes induced by gardening on the gut microbiota contribute to human health., (© 2022. The Author(s).)

Background: Diet affects the human gastrointestinal microbiota. Blood and urine samples have been used to determine nutritional biomarkers. However, there is a dearth of knowledge on the utility of fecal biomarkers, including microbes, as biomarkers of food intake., Objectives: This study aimed to identify a compact set of fecal microbial biomarkers of food intake with high predictive accuracy., Methods: Data were aggregated from 5 controlled feeding studies in metabolically healthy adults (n = 285; 21-75 y; BMI 19-59 kg/m2; 340 data observations) that studied the impact of specific foods (almonds, avocados, broccoli, walnuts, and whole-grain barley and whole-grain oats) on the human gastrointestinal microbiota. Fecal DNA was sequenced using 16S ribosomal RNA gene sequencing. Marginal screening was performed on all species-level taxa to examine the differences between the 6 foods and their respective controls. The top 20 species were selected and pooled together to predict study food consumption using a random forest model and out-of-bag estimation. The number of taxa was further decreased based on variable importance scores to determine the most compact, yet accurate feature set., Results: Using the change in relative abundance of the 22 taxa remaining after feature selection, the overall model classification accuracy of all 6 foods was 70%. Collapsing barley and oats into 1 grains category increased the model accuracy to 77% with 23 unique taxa. Overall model accuracy was 85% using 15 unique taxa when classifying almonds (76% accurate), avocados (88% accurate), walnuts (72% accurate), and whole grains (96% accurate). Additional statistical validation was conducted to confirm that the model was predictive of specific food intake and not the studies themselves., Conclusions: Food consumption by healthy adults can be predicted using fecal bacteria as biomarkers. The fecal microbiota may provide useful fidelity measures to ascertain nutrition study compliance., (© The Author(s) 2020. Published by Oxford University Press on behalf of American Society for Nutrition.)

How long-term dietary intake shapes microbiota composition and stability in young children is poorly understood. Herein, the temporal variability in stool microbiota composition in relation to habitual dietary patterns of 4- to 8-year-old children (n=22) was investigated. Fecal samples were collected at baseline, 6 weeks and 6 months. Bacterial composition and volatile fatty acids were assessed by 16S rRNA sequencing and gas-chromatography, respectively. Nutrient intake was assessed using 3-day food diaries and dietary patterns were empirically derived from a food frequency questionnaire. Using a factor loading of >0.45 for a food group to be a major contributor to the overall dietary pattern, two dietary patterns were found to be associated with distinct microbiome composition. Dietary Pattern 1 (DP1), characterized by intake of fish, protein foods, refined carbohydrates, vegetables, fruit, juice and sweetened beverages, kid's meals and snacks and sweets, was associated with higher relative abundance of Bacteroidetes, Bacteroides and Ruminococcus and lower abundance of Bifidobacterium, Prevotella, Blautia and Roseburia. Dietary Pattern 2 (DP2), characterized by intake of grains, dairy and legumes, nuts and seeds, was associated with higher relative abundance of Cyanobacteria and Phascolarctobacterium and lower abundance of Dorea and Eubacterium. Fruit and starchy foods were present in both patterns, but were more associated with DP1 and DP2, respectively. Temporal stability of microbiota over a 6-month period was associated with baseline dietary patterns. Understanding how dietary intake contributes to microbiota composition and stability in early life in important for dietary recommendations and designing clinical interventions for microbiota-associated diseases., (Copyright © 2018. Published by Elsevier Inc.)

OBJECTIVE To determine effects of restriction feeding of a moderate-protein, high-fiber diet on loss of body weight (BW), voluntary physical activity, body composition, and fecal microbiota of overweight cats. ANIMALS 8 neutered male adult cats. PROCEDURES After BW maintenance for 4 weeks (week 0 = last week of baseline period), cats were fed to lose approximately 1.5% of BW/wk for 18 weeks. Food intake (daily), BW (twice per week), body condition score (weekly), body composition (every 4 weeks), serum biochemical analysis (weeks 0, 1, 2, 4, 8, 12, and 16), physical activity (every 6 weeks), and fecal microbiota (weeks 0, 1, 2, 4, 8, 12, and 16) were assessed. RESULTS BW, body condition score, serum triglyceride concentration, and body fat mass and percentage decreased significantly over time. Lean mass decreased significantly at weeks 12 and 16. Energy required to maintain BW was 14% less than National Research Council estimates for overweight cats and 16% more than resting energy requirement estimates. Energy required for weight loss was 11% more, 6% less, and 16% less than American Animal Hospital Association recommendations for weight loss (80% of resting energy requirement) at weeks 1 through 4, 5 through 8, and 9 through 18, respectively. Relative abundance of Actinobacteria increased and Bacteroidetes decreased with weight loss. CONCLUSIONS AND CLINICAL RELEVANCE Restricted feeding of a moderate-protein, high-fiber diet appeared to be a safe and effective means for weight loss in cats. Energy requirements for neutered cats may be overestimated and should be reconsidered.

Background: Prebiotics resist digestion, providing fermentable substrates for select gastrointestinal bacteria associated with health and well-being. Agave inulin differs from other inulin type fibers in chemical structure and botanical origin. Preclinical animal research suggests these differences affect bacterial utilization and physiologic outcomes. Thus, research is needed to determine whether these effects translate to healthy adults., Objective: We evaluated agave inulin utilization by the gastrointestinal microbiota by measuring fecal fermentative end products and bacterial taxa., Methods: A randomized, double-blind, placebo-controlled, 3-period, crossover trial was undertaken in healthy adults (n = 29). Participants consumed 0, 5.0, or 7.5 g agave inulin/d for 21 d with 7-d washouts between periods. Participants recorded daily dietary intake; fecal samples were collected during days 16-20 of each period and were subjected to fermentative end product analysis and 16S Illumina sequencing., Results: Fecal Actinobacteria and Bifidobacterium were enriched (P < 0.001) 3- and 4-fold after 5.0 and 7.5 g agave inulin/d, respectively, compared with control. Desulfovibrio were depleted 40% with agave inulin compared with control. Agave inulin tended (P < 0.07) to reduce fecal 4-methyphenol and pH. Bivariate correlations revealed a positive association between intakes of agave inulin (g/kcal) and Bifidobacterium (r = 0.41, P < 0.001). Total dietary fiber intake (total fiber plus 0, 5.0, or 7.5 g agave inulin/d) per kilocalorie was positively associated with fecal butyrate (r = 0.30, P = 0.005), tended to be positively associated with Bifidobacterium (r = 0.19, P = 0.08), and was negatively correlated with Desulfovibrio abundance (r = -0.31, P = 0.004)., Conclusions: Agave inulin supplementation shifted the gastrointestinal microbiota composition and activity in healthy adults. Further investigation is warranted to determine whether the observed changes translate into health benefits in human populations. This trial was registered at clinicaltrials.gov as NCT01925560., (© 2015 American Society for Nutrition.)

Background: Prebiotic-containing infant formula may beneficially affect gastrointestinal tolerance and commensal microbiota composition., Objective: Assess gastrointestinal tolerance and fecal microbiota, pH, and short-chain fatty acid (SCFA) concentrations of infants consuming formula with or without prebiotics., Design: Full-term formula-fed infants were studied to a breastfed comparison group (BF). Formula-fed infants (FF) were randomized to consume a partially hydrolyzed whey formula with (PRE) or without (CON) 4 g/L of galacto-oligosaccharides and fructo-oligosaccharides (9:1). Fecal bacteria, pH, and SCFA were assessed at baseline, 3 weeks, and 6 weeks. Caregivers of patients recorded stool characteristics and behavior for 2 days before the 3- and 6-week visits., Results: Feces from infants fed PRE had a higher absolute number (P = .0083) and proportion (P = .0219) of bifidobacteria than CON-fed infants and did not differ from BF. BF had a higher proportion of bifidobacteria than CON (P = .0219) and lower number of Clostridium difficile than FF (P = .0087). Feces from formula-fed infants had higher concentrations of acetate (P < .001), butyrate (P < .001), propionate (P < .001), and total SCFAs (P = .0230) than BF; however, fecal pH was lower (P = .0161) in PRE and BF than CON. Prebiotic supplementation did not alter stool patterns, tolerance, or growth. BF had more frequent stools that were yellow (P < .0001) and more often liquid than FF (P < .0001)., Conclusions: Infant formula containing the studied oligosaccharides was well tolerated, increased abundance and proportion of bifidobacteria, and reduced fecal pH in healthy infants.

Introduction: Prevalence of chronic hypohydration remains elevated among adults in the USA; however, the health effects of hypohydration in regards to human gut health have not been explored. Methods: This study examined the relationship between total water intake, hydration biomarkers (first-morning urine specific gravity [FMUsg], first-morning urine volume [FMUvol], and plasma copeptin), fecal microbiota, and plasma lipopolysaccharide-binding protein (LBP) in adults (25–45 years, 64% female). Fecal microbiota composition was assessed using 16S rRNA gene sequencing (V4 region). Immunoassays quantified plasma copeptin and LBP in fasted venous blood samples. Dietary variables were measured using 7-day food records. Linear discriminant analysis effect size (LEfSe) analyzed differentially abundant microbiota based on median cutoffs for hydration markers. Multiple linear regressions examined the relationship between LBP and copeptin. Results: LEfSe identified 6 common taxa at the genus or species level that were differentially abundant in FMUsg, total water (g/day), or plasma copeptin (µg/mL) groups when split by their median values. Uncultured species in the Bacteroides, Desulfovibrio, Roseburia, Peptococcus, and Akkermansia genera were more abundant in groups that might indicate poorer hydration status. Multivariate linear analyses revealed a positive relationship between plasma copeptin and LBP when controlling confounding variables (F(6,52) = 4.45, p = 0.002, R2 = 0.34). Conclusions: Taxa common between markers are associated with the intestinal mucus layer, which suggests a potential link between hydration status and intestinal mucus homeostasis. The relationship between LBP and copeptin indicates that copeptin may be sensitive to metabolic endotoxemia and potentially gut barrier function. [ABSTRACT FROM AUTHOR]

Background: Obesity is associated with compromised intestinal barrier function and shifts in gastrointestinal microbiota that may contribute to inflammation. Fiber provides benefits, but impacts of fiber type are not understood.Objective: We aimed to determine the impact of cellulose compared with fructans on the fecal microbiota and gastrointestinal physiology in obese mice.Methods: Eighteen-wk-old male diet-induced obese C57BL/6J mice (n = 6/group; 40.5 g) were fed high-fat diets (45% kcal fat) containing 5% cellulose (control), 10% cellulose, 10% short-chain fructooligosaccharides (scFOS), or 10% inulin for 4 wk. Cecal and colon tissues were collected to assess barrier function, histomorphology, and gene expression. Fecal DNA extracts were subjected to 16S ribosomal RNA amplicon-based Illumina MiSeq sequencing to assess microbiota.Results: Body weight gain was greater (P < 0.05) in scFOS-fed than in 10% cellulose-fed mice. Both groups of fructan-fed mice had greater (P < 0.05) cecal crypt depth (scFOS: 141 μm; inulin: 145 μm) than both groups of cellulose-fed mice (5% and 10%: 109 μm). Inulin-fed mice had greater (P < 0.05) cecal transmural resistance (101 Ω × cm(2)) than 5% cellulose-fed controls (45 Ω × cm(2)). Inulin-fed mice had lower (P < 0.05) colonic mRNA abundance of Ocln (0.41) and Mct1 (0.35) than those fed 10% cellulose (Ocln: 1.28; Mct1: 0.90). Fructan and cellulose groups had different UniFrac distances of fecal microbiota (P < 0.05) and α diversity, which demonstrated lower (P < 0.01) species richness in fructan-fed mice. Mice fed scFOS had greater (P < 0.05) Actinobacteria (15.9%) and Verrucomicrobia (Akkermansia) (17.0%) than 5% controls (Actinobacteria: 0.07%; Akkermansia: 0.08%). Relative abundance of Akkermansia was positively correlated (r = 0.56, P < 0.01) with cecal crypt depth.Conclusions: Fructans markedly shifted gut microbiota and improved intestinal physiology in obese mice, but the mechanisms by which they affect gut integrity and inflammation in the obese are still unknown. [ABSTRACT FROM AUTHOR]

Background: In our published randomized, double-blind, placebo-controlled, 3-period crossover trial, healthy adult men (n = 21) consumed bars containing no supplemental fiber (placebo; NFC), poly-dextrose (21 g/d), and soluble corn fiber (SCF; 21 g/d) for 21 d each. Fecal specimens were collected between days 16 and 21 for fermentative end-product analysis and 16S ribosomal RNA bacterial gene amplification for bacterial taxa identification. Fiber supplementation decreased fecal putrefaction compounds and shifted abundances of several bacterial taxa. Objective: The objective was to perform whole-genome shotgun 454 pyrosequencing on the same fecal specimens collected in that clinical trial to obtain comprehensive fecal bacterial genome sequencing coverage and explore the full range of bacterial genetic information in the fecal microbiome, thereby using a systematic approach to study the impact of dietary fiber supplementation on fecal metabolites, bacterial taxa, and bacterial metagenomes. Design: Fecal samples were subjected to whole-genome shotgun 454 pyrosequencing to identify both fecal bacterial populations present and their functional genetic capacity. Results: Whole-genome shotgun sequencing results revealed that fiber consumption shifted the Bacteroidetes:Firmicutes ratio, increasing the relative abundance of Bacteroidetes 12 ± 2% and 13 ± 2% with polydextrose and SCF, respectively, compared with NFC. Bivariate correlations showed a positive correlation between the Bacteroidetes: Firmicutes ratio and total dietary fiber intake but not body mass index. Principal coordinates analysis of Bray-Curtis distances indicated that bacterial gene composition was more similar in participants consuming fibers (polydextrose and SCF combined) in comparison with NFC. Shifts in bacterial gene abundances after polydextrose and SCF supplementation included genes associated with carbohydrate, amino acid, and lipid metabolism, as well as metabolism of cofactors and vitamins. Conclusion: This study conveys novel information about the impact of dietary fiber supplementation on the phylogenetic structure and functional capacity of the fecal microbiome of healthy adults. This trial was registered at clinicaltrials.gov as NCT02091349. [ABSTRACT FROM AUTHOR]

The human gastrointestinal microbiota is increasingly linked to health outcomes; however, our understanding of how specific foods alter the microbiota is limited. Cruciferous vegetables such as broccoli are a good source of dietary fiber and phytonutrients, including glucosinolates, which can be metabolized by gastrointestinal microbes. This study aimed to determine the impact of broccoli consumption on the gastrointestinal microbiota of healthy adults. A controlled feeding, randomized, crossover study consisting of two 18-day treatment periods separated by a 24-day washout was conducted in healthy adults (n=18). Participants were fed at weight maintenance with the intervention period diet including 200 g of cooked broccoli and 20 g of raw daikon radish per day. Fecal samples were collected at baseline and at the end of each treatment period for microbial analysis. Beta diversity analysis indicated that bacterial communities were impacted by treatment (P=.03). Broccoli consumption decreased the relative abundance of Firmicutes by 9% compared to control (P=.05), increased the relative abundance of Bacteroidetes by 10% compared to control (P=.03) and increased Bacteroides by 8% relative to control (P=.02). Furthermore, the effects were strongest among participants with body mass index <26 kg/m2, and within this group, there were associations between bacterial relative abundance and glucosinolate metabolites. Functional prediction revealed that broccoli consumption increased the pathways involved in the functions of the endocrine system (P=.05), transport and catabolism (P=.04), and energy metabolism (P=.01). These results reveal that broccoli consumption affects the composition and function of the human gastrointestinal microbiota. [ABSTRACT FROM AUTHOR]