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Dietary consumption of prunes has favorable impacts on bone health, but more research is necessary to improve upon study designs and refine our understandings.We evaluated the effects of prunes (50 g or 100 g/d) on bone mineral density (BMD) in postmenopausal women during a 12-mo dietary intervention. Secondary outcomes include effects on bone biomarkers.The single-center, parallel-arm 12-mo randomized controlled trial tested the effects of 50 g and 100 g prunes compared with a control group on BMD (every 6 mo) and bone biomarkers in postmenopausal women.In total, 235 women (age 62.1 ± 5.0 y) were randomly allocated into control (n = 78), 50-g prune (n = 79), or 100-g prune (n = 78) groups. Compliance was 90.2 ± 1.8% and 87.1 ± 2.1% in the 50-g and 100-g prune groups. Dropout was 22%; however, the dropout rate was 41% for the 100-g prune group (compared with other groups: 10%, control; 15%, 50 g prune; P 0.001). A group × time interaction for total hip BMD was observed in control compared with 50-g prune groups (P 0.05) but not in control compared with 100-g prune groups (P 0.05). Total hip BMD decreased -1.1 ± 0.2% in the control group at 12 mo, whereas the 50-g prune group preserved BMD (-0.3 ± 0.2%) at 12 mo (P 0.05). Although hip fracture risk (FRAX) worsened in the control group at 6 mo compared with baseline (10.3 ± 0.5% compared with 9.8 ± 0.5%, P 0.05), FRAX score was maintained in the pooled (50 g + 100 g) prune groups.A 50-g daily dose of prunes can prevent loss of total hip BMD in postmenopausal women after 6 mo, which persisted for 12 mo. Given that there was high compliance and retention at the 50-g dosage over 12 mo, we propose that the 50-g dose represents a valuable nonpharmacologic treatment strategy that can be used to preserve hip BMD in postmenopausal women and possibly reduce hip fracture risk. This trial was registered at clinicaltrials.gov as NCT02822378.

Prunes have health benefits, particularly in postmenopausal women. It is likely that the gut microbiome mediates some of these effects, but its exact role remains to be elucidated. This study aims to characterize the effect of prune supplementation on the gut microbiome of postmenopausal women. The fecal microbiome of 143 postmenopausal women ages 55-75 who met the compliance criteria in a randomized controlled trial of a 12-month dietary intervention in one of three treatment groups - no prunes (

Effect of xylanase (Xyl) and live yeast (LY) supplementation on gut microbiome composition, growth performance, and nutrient digestibility of weanling pigs was determined. A total of 180 weanling pigs were assigned to five treatments from weaning to market. Treatments were designated based on whether Xyl, LY, or their combination were fed in the first 2 wk postweaning or thereafter until finishing at day 141 postweaning. Treatments were (days 1–15; days 15–141): control–control, control–Xyl, Xyl–Xyl, LY–Xyl, Xyl + LY–Xyl. Xylanase was added at 16 000 BXU·kg−1 and LY at 1 kg·t−1. Pigs fed with LY and LY + Xyl from days 0–15 had greater body weight and average daily gain at day 15 compared with control (P

Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems. Managing agricultural microbiomes is an efficient approach to improve crop performance in agroecosystems. This Review summarizes the current state of knowledge from less to more targeted approaches to manage soil, plant and pest-associated microbiomes. The authors also identify the knowledge gaps in relation to current agricultural practices in microbiome management.

Inflammatory bowel diseases (IBDs) including colitis are intestinal disorders characterized by chronic inflammation, barrier dysfunction and dysbiosis. Specific forms of vitamin E have been shown to attenuate colitis, but the mechanisms are not fully understood. The objective of this study is to examine the impact of α-tocopherol (αT) and γ-tocopherol-rich tocopherols (γTmT) on gut inflammation, barrier integrity and microbiota in dextran sulfate sodium (DSS)-induced colitis in mice. We observe that αT and γTmT mitigated DSS-caused fecal bleeding, diarrhea and elevation of IL-6. These vitamin E forms inhibited colitis-induced loss of the tight junction protein occludin, and attenuated colitis-caused elevation of LPS-binding protein in the plasma, a surrogate marker of intestinal barrier dysfunction, suggesting protection of gut barrier integrity. Consistently, αT and γT mitigated TNF-α/IFN-γ-induced impairment of trans-epithelial electrical resistance in human intestinal epithelial Caco-2 cell monolayer. Using 16S rRNA gene sequencing of fecal DNA, we observe that DSS reduced gut microbial evenness and separated microbial composition from healthy controls. In colitis-induced mice, γTmT but not αT separated gut microbial composition from controls, and attenuated DSS-caused depletion of Roseburia, which contains butyrate producing bacteria and is decreased in IBD patients. Canonical correspondence analysis also supports that γTmT favorably altered gut microbial community. In contrast, neither αT nor γTmT affected gut microbes in healthy animals. These results provide evidence supporting protective effects of αT and γT on intestinal barrier function and that γTmT caused favorable changes of the gut microbiota in colitis-induced mice.

Effect of timing of xylanase supplementation to weanling pigs and its effect on growth performance, nutrient digestibility, and fecal microbiota was investigated. A total of 128 weanling pigs [(Hampshire × Duroc) × (Yorkshire × Landrace); 6.2 ± 0.6 kg body weight (BW); weaning age: 21 d] were assigned to four treatments, with eight replicate pens and four pigs per pen. Treatments were a combination of two dietary treatments (without or with xylanase) in two periods; (period 1, days 0–14) and period 2 (days 14–42): xylanase–xylanase, xylanase–control, control–xylanase, and control–control. Fecal microbiota diversity and apparent total tract digestibility (ATTD) were determined. From days 0–14, pigs had lower (P

The efficacy of exogenous carbohydrases in pig diets has been suggested to depend on enzyme activity and dietary fiber composition, but recent evidence suggests other factors such as ambient temperature might be important as well. Therefore, we investigated the effect of heat stress (HS) on the efficacy of a multienzyme carbohydrase blend in growing pigs. Ninety-six (barrows: gilts; 1:1) growing pigs with initial body weight (BW) of 20.15 ± 0.18 kg were randomly assigned to six treatments, with eight replicates of two pigs per pen in a 3 × 2 factorial arrangement: three levels of carbohydrase (0, 1X, or 2X) at two environmental temperatures (20 °C or cyclical 28 °C nighttime and 35 °C day time). The 1X dose (50 g/tonne) provided 1,250 viscosimetry unit (visco-units) endo-β-1,4-xylanase, 4,600 units α-l-arabinofuranosidase and 860 visco-units endo-1,3(4)-β-glucanase per kilogram of feed. Pigs were fed ad libitum for 28 d and 1 pig per pen was sacrificed on day 28. There was no enzyme × temperature interaction on any response criteria; thus, only main effects are reported. Enzyme treatment quadratically increased (P < 0.05) BW on day 28, average daily gain (ADG) (P < 0.05), and average daily feed intake (ADFI) (P < 0.05) with the 1X level being highest. HS reduced the BW at day 14 (P < 0.01) and day 28 (P < 0.01), ADG (P < 0.01), and ADFI (P

Water clarity is often the primary guiding factor in determining whether a prefiltration step is needed to increase volumes processed for a range of microbial endpoints. In this study, we evaluate the effect of filter pore size on the bacterial communities detected by 16S rRNA gene sequencing and incidence of two host-specific microbial source tracking (MST) markers in a range of coastal waters from southern Lake Michigan, using two independent data sets collected in 2015 (bacterial communities) and 2016–2017 (MST markers). Water samples were collected from river, shoreline, and offshore areas. For bacterial communities, each sample was filtered through a 5.0-μm filter, followed by filtration through a 0.22-μm filter, resulting in 70 and 143 filter pairs for bacterial communities and MST markers, respectively. Following DNA extraction, the bacterial communities were compared using 16S rRNA gene amplicons of the V3–V4 region sequenced on a MiSeq Illumina platform. Presence of human (Bacteroides HF183) and gull (Gull2, Catellicoccus marimammalium) host-specific MST markers were detected by qPCR. Actinobacteriota, Bacteroidota, and Proteobacteria, collectively represented 96.9% and 93.9% of the relative proportion of all phyla in the 0.22- and 5.0-μm pore size filters, respectively. There were more families detected in the 5.0-μm pore size filter (368) than the 0.22-μm (228). There were significant differences in the number of taxa between the two filter sizes at all levels of taxonomic classification according to linear discriminant analysis (LDA) effect size (LEfSe) with as many as 986 taxa from both filter sizes at LDA effect sizes greater than 2.0. Overall, the Gull2 marker was found in higher abundance on the 5.0-μm filter than 0.22 μm with the reverse pattern for the HF183 marker. This discrepancy could lead to problems with identifying microbial sources of contamination. Collectively, these results highlight the importance of analyzing pre- and final filters for a wide range of microbial endpoints, including host-specific MST markers routinely used in water quality monitoring programs. Analysis of both filters may increase costs but provides more complete genomic data via increased sample volume for characterizing microbial communities in coastal waters.

Termites are eusocial insects that host a range of prokaryotic and eukaryotic gut symbionts and can differentiate into a range of caste phenotypes. Soldier caste differentiation from termite workers follows two successive molts (worker–presoldier–soldier) that are driven at the endocrine level by juvenile hormone (JH). Although physiological and eusocial mechanisms tied to JH signaling have been studied, the role of gut symbionts in the caste differentiation process is poorly understood. Here, we used the JH analog methoprene in combination with the antibiotic kanamycin to manipulate caste differentiation and gut bacterial loads in Reticulitermes flavipes termites via four bioassay treatments: kanamycin, methoprene, kanamycin+methoprene, and an untreated (negative) control. Bioassay results demonstrated a significantly higher number of presoldiers in the methoprene treatment, highest mortality in kanamycin+methoprene treatment, and significantly reduced protist numbers in all treatments except the untreated control. Bacterial 16S rRNA gene sequencing provided alpha and beta diversity results that mirrored bioassay findings. From ANCOM analysis, we found that several bacterial genera were differentially abundant among treatments. Finally, follow-up experiments showed that if methoprene and kanamycin or untreated termites are placed together, zero or rescued presoldier initiation, respectively, occurs. These findings reveal that endogenous JH selects for symbiont compositions required to successfully complete presoldier differentiation. However, if the gut is voided before the influx of JH, it cannot select for the necessary symbionts that are crucial for molting. Based on these results, we are able to provide a novel example of linkages between gut microbial communities and host phenotypic plasticity.

Consuming polyphenol-rich fruits and vegetables, including blueberries, is associated with beneficial health outcomes. Interest in enhancing polyphenol intakes via dietary supplements has grown, though differences in fruit versus supplement matrix on gut microbiota and ultimate phenolic metabolism to bioactive metabolites are unknown. To evaluate this, 5-month-old, ovariectomized, Sprague-Dawley rats were gavaged for 90 d with a purified extract of blueberry polyphenols (0, 50, 250, or 1000 mg total polyphenols per kg bw per d) or lyophilized blueberries (50 mg total polyphenols per kg bw per d, equivalent to 150 g fresh blueberries per day in humans). Urine, feces, and tissues were assessed for gut microbiota and phenolic metabolism. Significant dose- and food matrix-dependent effects were observed at all endpoints measured. Gut microbial populations showed increased diversity at moderate doses but decreased diversity at high doses. Urinary phenolic metabolites were primarily observed as microbially derived metabolites and underwent extensive host xenobiotic phase II metabolism. Thus, blueberry polyphenols in fruit and supplements induce differences in gut microbial communities and phenolic metabolism, which may alter intended health effects.

OBJECTIVES: The adolescent period is crucial for optimizing future bone health because during these years bone accumulates rapidly accounting for up to half of adult peak bone mass (PBM). Calcium intake during this stage is critical for adequate bone mineralization but this essential nutrient, the major constituent of hydroxyapatite, is usually inadequate in the diets of US adolescents. A strategy to maximize bone mineralization is to increase calcium absorption. This could be achieved by soluble corn fiber (SCF) supplementation, which fermentation through bacteria in the lower intestine produces short-chain fatty acids and increase calcium absorption. However, there are no studies determining the long-term effects of SCF on bone mass in children. The main aim of the MetA-Bone Trial is to determine the effect of one-year SCF supplementation compared to placebo on bone mass in children with low habitual calcium intake. We hypothesize that SCF supplementation will result in a higher Bone Mineral Content. We will also determine the effects of SCF supplementation on bone biomarkers; we hypothesize that supplementation with SCF will result in higher levels of bone formation and lower bone resorption biomarkers. METHODS: A total of 240 healthy children (10–13 years), with usual low dietary calcium, will be randomized to four experimental groups for 1 year: (1) SCF (12 g/d); (2) SCF (12 g/d) + 600 mg/d of calcium; (3) Placebo (maltodextrin); and (4) Placebo + 600 mg/d of calcium. The supplements will be mixed with a flavored powder beverage to dilute in water and participants will be instructed to drink this twice per day. Bone mass will be measured using dual energy x-ray absorptiometry (DXA) at baseline, 6 and 12 months. Serum bone biomarkers will be measured at baseline and at 12 months. RESULTS: NA CONCLUSIONS: If supplementing diets with SCF lead to higher bone mass during adolescence, this could help achieve the genetic potential for PBM and to start adult life with stronger bones. Incorporating SCF into diets may be a cost-effective intervention for bone health than increasing dairy products consumption, particularly in adolescents. FUNDING SOURCES: Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health.

Hydro-meteorological conditions facilitate transport of fecal indicator bacteria (FIB) to the nearshore environment, affecting recreational water quality. North Beach (Racine, Wisconsin, United States), is an exemplar public beach site along Lake Michigan, where precipitation-mediated surface runoff, wave encroachment, stormwater and tributary outflow were demonstrated to contribute to beach advisories. Multiple restoration actions, including installation of a stormwater retention wetland, were successfully deployed to improve recreational water quality. Implementation of molecular methods (e.g. human microbial source tracking markers and Escherichia coli (E. coli) qPCR) assisted in identifying potential pollution sources and improving public health response time. However, periodic water quality failures still occur. As local beach managers reassess restoration measures in response to climatic changes, use of expanded microbial methods (including bacterial community profiling) may contribute to a better understanding of these dynamic environments. In this 2-year study (2015 and 2019), nearshore/offshore Lake Michigan, stormwater, and tributary samples were collected to determine if, 1) the constructed wetland (~50 m from the shoreline) continued to provide stormwater separation/retention and 2) mixing between onshore sources, Root River and Lake Michigan, was increasing due to rising precipitation/lake levels. Monthly rainfall totals were 1.5× higher in 2019 than 2015, coinciding with a 0.63 m lake-level rise. The prevalence of more intense, onshore winds also increased, facilitating interaction between potential reservoirs of FIB with nearshore water through wind driven waves and lake intrusion, e.g. beach sands and the adjacent Root River. While a strong relationship existed between wet weather wetland and North Beach nearshore E. coli concentrations (all sites), bacterial communities were strikingly different. Conversely, bacterial community overlap existed between the Root River mouth and nearshore/offshore sites. These results suggest the constructed wetland can accommodate the climate-related changes observed in this study. Future restoration activities could be directed towards upstream tributary sources in order to minimize microbial contaminants entering Lake Michigan.

Calcium intake is critical for adequate bone mineralization in adolescence, but it is usually inadequate in US adolescents. A strategy to maximize bone mineralization is to increase calcium absorption, which could be achieved by soluble corn fiber (SCF). There are no studies determining the long-term effects of SCF on bone mass in children. Objectives To determine the effect of one-year SCF supplementation compared to placebo on bone mass and bone biomarkers in children with low habitual calcium intake. We hypothesize that SCF supplementation will result in a higher bone mineral content and higher levels of bone formation and lower bone resorption biomarkers. Methods 240 healthy children (10–13 years), with usual low calcium intake, will be randomized to four experimental groups for 1 year: (1) SCF (12 g/d); (2) SCF (12 g/d) + 600 mg/d of calcium; (3) Placebo (maltodextrin); and (4) Placebo +600 mg/d of calcium. The supplements have been pre-mixed with a flavored powder beverage and participants will only need to dilute it in water and drink this twice per day. Bone will be measured using dual energy x-ray absorptiometry (DXA) at baseline, 6 and 12 months. Serum bone biomarkers will be measured at baseline and at 12 months. Conclusions If supplementing diets with SCF lead to higher bone mass during adolescence, this could help achieve the genetic potential for PBM and to start adult life with stronger bones. If successful, SCF can be incorporated into diets for promoting bone health in adolescents.

Cover crop adoption in the U.S. Corn Belt region is a rapidly emerging management practice in corn (Zea mays) agroecosystems. However, little is known about the impact of the inclusion of cover crops on the soil microbiome and its relation to the decomposition of the cover crop residue during the cash crop growing season. Therefore, this study sought to determine the impact of cover crop species and residue management practices on soil microbial community composition and structure during winter cover crop decomposition over the corn growing season. Cover crop treatments included hairy vetch (Vicia villosa Roth), cereal rye (Secale cereal), a hairy vetch/cereal rye mixture, and a no cover crop control. Residue management practices included no-tillage and a 15 cm reduced spring tillage following cover crop termination. Soil samples were collected at five dates during cover crop decomposition that corresponded to an accumulated number of calendar days from cover crop termination, and soil bacterial communities were characterized using the small subunit (16S) rRNA gene sequences. Statistical analyses revealed that sampling date, cover crop treatment, and residue management treatment were significant determinants of soil microbial community composition (p 2.0). Data generated from this study leads to a deeper understanding of bacterial responses to cover crop decomposition in corn agroecosystems.

Invasive woody plant species are a threat to biodiversity and ecosystem function in forests of the eastern U.S., due in part to their effects on soil properties and nutrient cycling. Controlling invasive shrubs can benefit the ecosystem at multiple scales, but these species tend to resprout when cut, and post-cutting flushes of root exudates have been linked to accelerated decomposition of soil organic matter (SOM), a rhizosphere priming effect. We removed the invasive shrub Lonicera maackii (Rupr.) Herder (Amur honeysuckle) from forested sites in central Indiana, USA, using cut-stump and forestry mulching head treatments. For two growing seasons after the initial removal treatments, we compared the soil chemistry and microbial community function of bulk and honeysuckle rhizosphere soils in shrub removal areas to those in invaded reference areas. Microbial activity measured using multiple substrate induced respiration (MSIR) in bulk soils was generally lower in removal areas than reference areas the first year, coinciding with relatively elevated responses in the rhizosphere soils of resprouting shrubs. Elevated SOM and organic C in rhizosphere soils of resprouting shrubs suggested a flush of rhizodeposits from cutting and regrowth. However, bulk soil chemistry responses to shrub removal did not show any evidence of a rhizosphere priming effect, but instead reflected the reduced effects of honeysuckle on throughfall precipitation chemistry—higher ammonium and lower magnesium. Nonetheless, changes in bulk soil chemistry between years were driven by the chemical characteristics of rhizosphere soil associated with resprouting honeysuckle. This study is the first to document the potential for invasive shrub control to affect soil properties through rhizodeposition by the target species.

Carryover effect of prior fibre consumption on metabolic markers was investigated. Treatments were arranged in 2 × 2 factorial with 2 fibre sources, 4% inulin or cellulose (Solka-Floc®) and fat levels (5 or 15%) for the low-fat diet (LFD) and high-fat diet (HFD) respectively. Pigs were fed the two fibre diets for the first 56d (nursery phase), and thereafter fed either the LFD or HFD containing no added fibre source from d56 to 140 (growing phase). Pigs on the HFD were heavier (p = .05) than those on LF (64.61 vs. 68.38 kg), regardless of prior fibre type consumed. Pigs that were fed cellulose during the nursery and later fed the HFD had the highest ADG (p < .05). Feeding the HFD resulted in higher back fat (BF) (13.41 and 18.18 ± 0.12 mm for LFD and HFD, respectively; p < .01). The HFD resulted in higher (p < .01) insulin (0.014 and 0.016 ± 0.001 mg/L for LF and HF respectively) and glucose (100.89 and 125.03 ± 4.39 mg/dl for LF and HF respectively) concentrations in the serum. Inulin increased (p ≤ .02) jejunal expression of SREBP-1c and CL-4, but reduced (p < .05) TNFɑ and IL-6 expression in the ileum. Alpha-diversity was significantly different (p < .05) between the inulin and cellulose fed pigs at the end of the nursery and finishing phases. Therefore, inulin feeding before a HFD may lead to reduction in ADG and inflammatory markers in the small intestine of pigs, and thus prevent future metabolic disorders.

Shoreline sand harbors high concentrations of fecal indicator bacteria (FIB) that may be resuspended into the water column through washing and resuspension. Studies have explored coastal processes that influence this sand-water flux for FIB, but little is known about how microbial markers of contamination or the bacterial community interact in the sand-water interface. In this study, we take a three-tiered approach to explore the relationship between bacteria in sand, sediment, and overlying water at three shoreline sites and two associated rivers along an extended freshwater shoreline. Samples were collected over two years and analyzed for FIB, two microbial source tracking (MST) markers (Catellicoccus marimammalium, Gull2; Bacteroides HF183), and targeted metagenomic 16S rRNA gene analysis. FIB was much higher in sand than in water at all three sites. Gull2 marker was abundant in shoreline sand and water while HF183 marker was mostly present in rivers. Overall bacterial communities were dissimilar between sand/sediment and water, indicating little interaction. Sediment composition was generally unfavorable to bacterial resuspension. Results show that FIB and MST markers were effective estimates of short-term conditions at these locations, and bacterial communities in sand and sediment reflected longer-term conditions. Findings are useful for locating contamination sources and targeting restoration by evaluating scope of shoreline degradation.

OBJECTIVES: Recent discoveries suggest that gut microbiota is involved in the progression of colitis-associated colorectal cancer (CAC) and natural products like polyphenols can modulate gut microbiota. Polyphenol components of grape like resveratrol have been shown to have anti-colorectal cancer effects in animal models, but the underlying mechanism is not completely understood. The objective of this study is to examine the chemo-preventive effect of a whole grape powder (GP) on tumorigenesis in a mouse CAC model and evaluated the impact of GP on gut microbiota as a potential anti-CAC mechanism. To dissect the role of polyphenols in the GP, we compared GP at 3 and 10% diet to calorie, fiber, sugar and organic acid-matched placebo. METHODS: We used male Balb/c mice and divided them into diseased groups treated with azoxymethane (AOM) and dextran sodium sulfate (DSS) and healthy groups, both of which had placebo control diet, GP at 3% or 10% diet. To induce tumorigenesis, we injected AOM at 9.5 mg/kg bw at 6 weeks of age, followed by 2-cycle DSS (1.5% in drinking water). During the study, we monitored animals’ body weight and food consumption weekly, and evaluated their colitis symptoms during DSS treatments. All animals were sacrificed at 16 weeks of age and 24-hr accumulative fecal samples were collected prior to sacrifice for gut microbial analysis. RESULTS: Compared to the control diet, 10% GP diet alleviated colitis symptoms including rectal bleeding and diarrhea, and reduced total tumor multiplicity by 29% (P

Crohn's Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future.

The gut microbiota play important roles in colon cancer. Vitamin E δ-tocotrienol (δTE) and its metabolite δTE-13'-carboxychromanol (δTE-13') are known to have cancer-preventive effects, but their impact on gut flora during tumorigenesis and the role of the metabolite in δTE's beneficial effects remain to be determined. In the murine colitis-associated colon cancer (CAC) induced by azoxymethane (AOM) and dextran sulfate sodium (DSS), we show that δTE and δTE-13' inhibited the multiplicity of large adenomas (>2 mm2) by 34% (P

The ecosystem of the human gastrointestinal (GI) tract traverses a number of environmental, chemical, and physical conditions because it runs from the oral cavity to the anus. These differences in conditions along with food or other ingested substrates affect the composition and density of the microbiota as well as their functional roles by selecting those that are the most suitable for that environment. Previous studies have mostly focused on Bacteria, with the number of studies conducted on Archaea, Eukarya, and Viruses being limited despite their important roles in this ecosystem. Furthermore, due to the challenges associated with collecting samples directly from the inside of humans, many studies are still exploratory, with a primary focus on the composition of microbiomes. Thus, mechanistic studies to investigate functions are conducted using animal models. However, differences in physiology and microbiomes need to be clarified in order to aid in the translation of animal model findings into the context of humans. This review will highlight Bacteria, Archaea, Fungi, and Viruses, discuss differences along the GI tract of healthy humans, and perform comparisons with three common animal models: rats, mice, and pigs.

BACKGROUND: Soluble corn fiber (SCF; 12 g fiber/d) is shown to increase calcium absorption efficiency, associated with shifts in the gut microbiota in adolescent males and females who participated in a controlled feeding study. OBJECTIVE: We evaluated the dose response of 0, 10, and 20 g fiber/d delivered by PROMITOR SCF 85 (85% fiber) on calcium absorption, biochemical bone properties, and the fecal microbiome in free-living adolescents. METHODS: Healthy adolescent females (n = 28; aged 11-14 y) randomly assigned into a 3-phase, double-blind, crossover study consumed SCF for 4 wk at each dose (0, 10, and 20 g fiber/d from SCF) alongside their habitual diet and were followed by 3-d clinical visits and 3-wk washout periods. Stable isotope ((44)Ca and (43)Ca) enrichment in pooled urine was measured by inductively coupled plasma mass spectrometry. Fecal microbial community composition was assessed by high-throughput sequencing (Illumina) of polymerase chain reaction-amplified 16S rRNA genes. Mixed model ANOVA and Friedman analysis were used to determine effects of SCF on calcium absorption and to compare mean microbial proportions, respectively. RESULTS: Calcium absorption increased significantly with 10 (13.3% ± 5.3%; P = 0.042) and 20 g fiber/d (12.9% ± 3.6%; P = 0.026) from SCF relative to control. Significant differences in fecal microbial community diversity were found after consuming SCF (operational taxonomic unit measures of 601.4 ± 83.5, 634.5 ± 83.8, and 649.6 ± 75.5 for 0, 10, and 20 g fiber/d, respectively; P < 0.05). Proportions of the genus Parabacteroides significantly increased with SCF dose (1.1% ± 0.8%, 2.1% ± 1.6%, and 3.0% ± 2.0% for 0, 10, and 20 g fiber/d from SCF, respectively; P < 0.05). Increases in calcium absorption positively correlated with increases in Clostridium (r = 0.44, P = 0.023) and unclassified Clostridiaceae (r = 0.40, P = 0.040). CONCLUSIONS: SCF, a nondigestible carbohydrate, increased calcium absorption in free-living adolescent females. Two groups of bacteria may be involved, one directly fermenting SCF and the second fermenting SCF metabolites further, thereby promoting increased calcium absorption. This trial was registered at clinicaltrials.gov as NCT01660503.

Restoration of degraded aquatic habitats is critical to preserve and maintain ecosystem processes and economic viability. Effective restoration requires contaminant sources identification. Microbial communities are increasingly used to characterize fecal contamination sources. The objective was to determine whether nearshore and adjacent beach bacterial contamination originated from the Grand Calumet River, a highly urbanized aquatic ecosystem, and to determine if there were correlations between pathogens/feces associated bacteria in any of the samples to counts of the pathogen indicator species Escherichia coli. Water samples were collected from the river, river mouth, nearshore, and offshore sites along southern Lake Michigan. Comparisons among communities were made using beta diversity distances (weighted and unweighted Unifrac, and Bray Curtis) and Principal Coordinate Analysis of 16S rRNA gene Illumina sequence data that indicated river bacterial communities differed significantly from the river mouth, nearshore lake, and offshore lake samples. These differences were further supported using Source Tracker software that indicated nearshore lake communities differed significantly from river and offshore samples. Among locations, there was separation by sampling date that was associated with environmental factors (e.g., water and air temperature, water turbidity). Although about half the genera (48.1%) were common to all sampling sites, linear discriminant analysis effect size indicated there were several taxa that differed significantly among sites; there were significant positive correlations of feces-associated genera with E. coli most probable numbers. Results collectively highlight that understanding microbial communities, rather than relying solely on select fecal indicators with uncertain origin, are more useful for developing strategies to restore degraded aquatic habitats.

Inflammatory bowel disease (IBD), comprised of Crohn's disease and ulcerative colitis, is a chronic inflammatory condition of multifactorial etiology and risk factors. Currently, one of the most effective treatments for IBD is the use of Tumor Necrosis Factor (TNF) functional inhibitor drugs, however, this treatment can cause adverse reactions and has a relatively large percentage of incomplete or non-responders. This lack of response may be related to differences in patients’ gut microbiomes prior to and after disease initiation or treatment. Recent observations in our lab using a rodent model of IBD support the theory that TNF drives acute colitis, but also that the microbiome differs in association with TNF production and colitis severity. Studies such as this and others provide new insights into host-microbiome interactions associated with colitis that can lead to new therapies to prevent or treat the disease.

Introduced, invasive plants can alter local soil chemistry and microbial communities, but the underlying mechanisms and extent of these changes are largely unknown. Based on characteristics associated with invasiveness in plants, it was hypothesized that introduced species that produce large amounts of litter with distinctive secondary compounds can a) alter the chemistry of both extractable and bulk carbon in the soil, b) shift microbial communities towards microbes better able to metabolize the compounds in the litter and c) cause soil carbon chemistry and microbial communities to shift to relatively uniform, novel states at multiple sites. Composition of phenolics in senescent tissues (leaves and roots) of Polygonum cuspidatum was compared to the composition of extractable phenolics and non-extractable bulk organic carbon in soils under and adjacent to large, long-established stands of P.cuspidatum at four sites in the eastern U.S. Rates of degradation of phenolics, activities of enzymes associated with the breakdown of phenolics and shifts in microbial community composition were also measured at the sites. Soils under P.cuspidatum stands contained twice as much phenolics as adjacent soils, but the composition of phenolics differed greatly between soils under stands and senescent tissues of P.cuspidatum. Flavonoids and proanthocyanidins constituted >90% of the identified phenolics in P.cuspidatum tissues, whereas monophenolic compounds accounted for >90% of the phenolics in soils under stands. Soils under and adjacent to stands also exhibited distinctive compositions of relatively persistent bulk organic carbon; composition differed less between soils under stands at different sites than between soils under and adjacent to stands at the same site. Soils under P.cuspidatum had 28 times greater abundance of fungi than soils adjacent to stands, and fungal markers showed clear separation of soils under and adjacent to P.cuspidatum. However, the potential activity of enzymes that degrade polyphenols was lower in soils under stands. Exogenously applied, chemically complex polyphenols persisted in both P.cuspidatum-invaded and adjacent non-invaded soils, whereas less complex compounds rapidly disappeared from both soils.Synthesis. Results suggest that interactions between plant inputs, abiotic reactions and biotic transformations may create and maintain new states in invaded soils that are chemically and biologically less diverse. In the case of polyphenol-rich, fast-growing invasive species, these interactions may alter the composition of bulk soil organic matter that has relatively slower turnover rates, resulting in legacy effects. Restoration could thus require, not just removal of the species, but also post-removal interventions such as soil amendments.

Resuscitation-promoting factor (Rpf) is a protein that has been found in a number of different Actinobacteria species and has been shown to promote the growth of active cells and resuscitate dormant (non-dividing) cells. We previously reported the biological activity of an Rpf protein in Tomitella biformata AHU 1821(T), an Actinobacteria isolated from a permafrost ice wedge. This protein is excreted outside the cell; however, few studies have investigated its contribution in environmental samples to the growth or resuscitation of bacteria other than the original host. Therefore, the aim of the present study was to determine whether Rpf from T. biformata impacted the cultivation of other bacteria from the permafrost ice wedge from which it was originally isolated. All experiments used recombinant Rpf proteins produced using a Rhodococcus erythropolis expression system. Dilutions of melted surface sterilized ice wedge samples mixed with different doses of the purified recombinant Rpf (rRpf) protein indicated that the highest concentration tested, 1250 pM, had a significantly (p

We present the draft genome sequence of the potential biocontrol agent Pseudomonas fluorescens TR3, which was isolated from rice leaves infected with Magnaporthe oryzae in a greenhouse. The genome of TR3 was assembled into 26 scaffolds (~6 Mbp) and includes genes potentially involved in bacterial interactions with fungi.

Mouse models are often used to determine the interactions between the microbiota and inflammatory processes and overcome the confounding effect of the naturally high inter-individual variation of the gut microbiota in humans. However, the microbiomes of mice are also variable and data detailing the degree to which factors like mouse sex and age contribute to mouse gut microbiota variation is limited. Our objective was to determine the impact sex and age have on the mouse gut microbiota and the severity of acute 2, 4, 6-trinitrobenzenesulfonic acid (TNBS) induced colitis. We used Illumina sequencing of 16S rRNA genes to characterize the fecal microbiota of B6.129S wild-type (WT) mice and mice lacking tumor necrosis factor (Tnf-/-) before and after acute TNBS colitis. There were differences between the fecal microbiota of male and female WT mice as well as Tnf-/- mice, both pre-and post-colitis. Male WT mice had more severe colitis than female WT mice and Tnf-/- mice of both sexes. We also identified microbial taxa differences between 4-5 and 6-7-week old WT and Tnf-/- mice both pre-and post-colitis. Here we provide evidence that the mouse fecal microbiome is shaped, in part, by sex, age and TNF production and that these effects correlate with the degree of animals' colitis.

This study was conducted to isolate and characterize soil microorganisms capable of solubilizing Chilembwe and Sinda rock phosphates readily available in Zambia. Single isolates were obtained by direct plating and enrichment cultures with succinate, cellulose and glucose as the carbon sources. Isolates were differentiated using colony morphology (form, margin, elevation and colour) and a subset of 20 was chosen for identification using the 16S rRNA gene sequences. After being cultured in nutrient broth and defined medium with tricalcium phosphate as the sole phosphate source, ten isolates were characterized for acid phosphatase enzyme activity. Over 80 isolates were obtained from different rock phosphate-sugar combinations. Isolates had varying morphological characteristics and the 20 strains identified showed a large diversity of organisms belonging to the genera Enterobacter, Burkholderia, Arthrobacter, Bacillus, Beijerinckia and two genera not previously reported to have P-solubilizing capabilities, Dyella and Curtobacterium. Both the observed growth and genera to which isolates belonged were dependent on the type of rock phosphate. Almost all isolates tested showed acid phosphatase activity that were similar to previously reported levels, ranging from 0.62 to 4.8 µg p-nitrophenol per 108 cells per hour. This work will be useful as the basis for the development of appropriate seed inocula that can enhance Sinda and Chilembwe rock phosphate dissolution and increased plant available P for crop production. Key words: Chilembwe, Sinda, Rock Phosphate, Burkholderia, Enterobacter, Rhizobia, Dyella, Arthrobacter, Curtobacterium, Dyella.

Functional variation of Rpf, a growth factor found exclusively in Actinobacteria, is differentiated by its source and amino acid sequences. Only purified Rpf proteins from three species have been studied so far. To seek new Rpfs for use in future studies to understand their role in Actinobacteria, the objective of this study was to identify rpf gene homologs in Tomitella biformata AHU 1821T, a novel Actinobacteria isolated from permafrost ice wedge. Amplification using degenerate primers targeting the essential Rpf domain led to the discovery of a new rpf gene in T. biformata. Gene structure and the deduced Rpf domain amino acid sequence indicated that this rpf gene was not identical to previously studied Rpf. Phylogenetic analysis placed T. biformata Rpf in a monophyletic branch in the RpfB subfamily. The deduced amino acid sequence was 44.9% identical to RpfB in Mycobacterium tuberculosis, the closest functionally tested Rpf. The gene was cloned and expressed in Escherichia coli; the recombinant Rpf protein (rRpf) promoted the growth of dividing cells and resuscitated non-dividing cells of T. biformata. Compared to other studies, this Rpf was required at higher concentrations to promote its growth and to resuscitate itself from a non-dividing state. The resuscitation function was likely due to the highly conserved Rpf domain. This study provides evidence that a genetically unique but functional Rpf can be found in novel members of Actinobacteria and can lead to a better understanding of bacterial cytokines in this phylum.

The yacon (Smallanthus sonchifolius) tuber was examined with regard to its prebiotic effects compared with commercialized fructo-oligosaccharides (FOS). A feed containing 10% yacon tuber, which is equivalent to 5% commercialized FOS in terms of the amount of fructo-oligosaccharides (GF2, GF3 and GF4), was administrated to rats for 28 days. The yacon diet changed the intestinal microbial communities beginning in the first week, resulting in a twofold greater concentration of cecal short-chain fatty acids (SCFAs). The SCFA composition differed, but the cecal pH in rats fed yacon tuber was equal to that in rats fed FOS. Serum triglycerides were lower in rats fed yacon compared with rats fed FOS and the control diet. Cecal size was greater with the yacon tuber diet compared with the control diet. The abundant fermentation in the intestines created a selective environment for the intestinal microbiota, which included Lactobacillus acidophilus, Bifidobacterium pseudolongum, Bifidobacterium animalis and Barnesiella spp. according to identification with culture-independent analysis, 16S rRNA gene PCR-DGGE combined with cloning and sequencing. Barnesiella spp. and B. pseudolongum were only found in the rats fed the yacon diet, while L. acidophilus and B. animalis were found in abundance in rats fed both the yacon and FOS diets. The genus Barnesiella has not previously been reported to be associated with yacon or FOS fermentation. We concluded that the physiological and microbiological effects of the yacon tuber were different from those of FOS. Differences in cecal size, blood triglycerides and microbial community profiles including their metabolites (SCFAs) between the yacon tuber and FOS were shown to be more greatly affected by the yacon tuber rather than FOS.

A great deal of research has been done to understand bacterial cell-to-cell signaling systems, but there is still a large gap in our current knowledge because the majority of microorganisms in natural environments do not have cultivated representatives. Metagenomics is one approach to identify novel quorum sensing (QS) systems from uncultured bacteria in environmental samples. In this study, fosmid metagenomic libraries were constructed from a forest soil and an activated sludge from a coke plant, and the target genes were detected using a green fluorescent protein (GFP)-based Escherichia coli biosensor strain whose fluorescence was screened by spectrophotometry. DNA sequence analysis revealed two pairs of new LuxI family N -acyl- l -homoserine lactone (AHL) synthases and LuxR family transcriptional regulators (clones N16 and N52, designated AubI/AubR and AusI/AusR, respectively). AubI and AusI each produced an identical AHL, N -dodecanoyl- l -homoserine lactone (C 12 -HSL), as determined by nuclear magnetic resonance (NMR) and mass spectrometry. Phylogenetic analysis based on amino acid sequences suggested that AusI/AusR was from an uncultured member of the Betaproteobacteria and AubI/AubR was very deeply branched from previously described LuxI/LuxR homologues in isolates of the Proteobacteria . The phylogenetic position of AubI/AubR indicates that they represent a QS system not acquired recently from the Proteobacteria by horizontal gene transfer but share a more ancient ancestry. We demonstrated that metagenomic screening is useful to provide further insight into the phylogenetic diversity of bacterial QS systems by describing two new LuxI/LuxR-type QS systems from uncultured bacteria.

Galactooligosaccharides (GOS), prebiotic nondigestible oligosaccharides derived from lactose, have the potential for improving mineral balance and bone properties. This study examined the dose-response effect of GOS supplementation on calcium and magnesium absorption, mineral retention, bone properties, and gut microbiota in growing rats. Seventy-five 4-week-old male Sprague-Dawley rats were randomized into one of five treatment groups (n = 15/group) and fed a diet containing 0, 2, 4, 6, or 8% GOS by weight for 8 weeks. Dietary GOS significantly decreased cecal pH and increased cecal wall weight and content weight in a dose-dependent manner (p < 0.0001). Fingerprint patterns of the 16S rRNA gene PCR-DGGE from fecal DNA indicated the variance of bacterial community structure, which was primarily explained by GOS treatments (p = 0.0001). Quantitative PCR of the samples revealed an increase in the relative proportion of bifidobacteria with GOS (p = 0.0001). Net calcium absorption was increased in a dose-response manner (p < 0.01) with GOS supplementation. Dietary GOS also increased (p < 0.02) net magnesium absorption, femur ⁴⁵Ca uptake, calcium and magnesium retention, and femur and tibia breaking strength. Distal femur total and trabecular volumetric bone mineral density (vBMD) and area and proximal tibia vBMD increased (p < 0.02) with GOS supplementation. Trabecular-rich bones, that is, those that rapidly turn over, were most benefited. Regression modeling showed that GOS benefited calcium and magnesium utilization and vBMD through decreased cecal pH, increased cecal wall and content weight, and increased proportion of bifidobacteria.

Multi-phase extraction (MPE) is commonly used at petroleum-contaminated sites to volatilize and recover hydrocarbons from the vadose and saturated zones in contaminant source areas. Although primarily a physical treatment technology, the induced subsurface air flow can potentially increase oxygen supply and promote aerobic biodegradation of benzene, toluene, ethylbenzene, and xylenes (BTEX), the contaminants of concern at gasoline-contaminated sites. In this study, real-time PCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles were used to elucidate the impact of MPE operation on the aquifer microbial community structure and function at a gasoline-contaminated site. Prior to system activation, ring-hydroxylating toluene monooxygenase (RMO) and naphthalene dioxygenase (NAH) gene copies were on the order of 106 to 1010 copies L−1 in groundwater samples obtained from BTEX-impacted wells. Aromatic oxygenase genes were not detected in groundwater samples obtained during continuous MPE indicating decreased populations of BTEX-utilizing bacteria. During periods of pulsed MPE, total aromatic oxygenase gene copies were not significantly different than prior to system activation, however, shifts in aromatic catabolic genotypes were noted. The consistent detection of RMO, NAH, and phenol hydroxylase (PHE), which catabolizes further oxidation of hydroxylated BTEX metabolites indicated the potential for aerobic biodegradation of dissolved BTEX during pulsed MPE.

Subsurface injection of oxygen-releasing materials (ORMs) is frequently performed at petroleum-contaminated sites to stimulate aerobic bioremediation of benzene, toluene, ethylbenzene, and xylenes (BTEX). In this study, qPCR enumeration of aromatic oxygenase genes and PCR-DGGE profiles of bacterial 16S rRNA genes were combined with groundwater monitoring to determine the impact of ORM injection on BTEX bioremediation at a gasoline-contaminated site. Prior to injection, BTEX concentrations were greater than 3 mg/L and DO levels were typically lessthan 2 mg/L, butphenol hydroxylase (PHE) and ring-hydroxylating toluene monooxygenase (RMO) genes were detected in impacted wells indicating the potential for aerobic BTEX biodegradation. Following injection, DO increased, BTEX concentrations decreased substantially, and PHE and RMO genes copies increased by 1-3 orders of magnitude. In addition, naphthalene dioxygenase (NAH) and xylene monooxygenase (TOL) genes were intermittently detected during periods of increased DO. Following depletion of the ORM, DO decreased, BTEX concentrations rebounded, and oxygenase genes were no longer detected. Temporal changes in PCR-DGGE microbial community profiles reflected the dynamic changes in subsurface conditions. Overall, the combination of chemical and geochemical analyses with quantification of aromatic oxygenase genes demonstrated that injection stimulated BTEX biodegradation until the ORM was depleted.