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Background Chronic alcohol consumption is associated with a compromised innate and adaptive immune response to infectious disease. Mucosa-associated invariant T (MAIT) cells play a critical role in antibacterial host defense. However, whether alcohol-associated deficits in innate and adaptive immune responses are mediated by alterations in MAIT cells remains unclear. Methods To investigate the impact of alcohol on MAIT cells, mice were treated with binge-on-chronic alcohol for 10 days and sacrificed at day 11. MAIT cells in the barrier organs (lung, liver and intestine) were characterized by flow cytometry. Two additional sets of animals were used to examine the involvement of gut microbiota on alcohol-induced MAIT cell changes. 1) Cecal microbiota from alcohol-fed (AF) mice were adoptive transferred into antibiotics-pretreated mice; 2) AF mice were treated with antibiotics during the experiment. MAIT cells in the barrier organs were measured via flow cytometry. Results Binge-on-chronic alcohol feeding led to a significant reduction in the abundance of MAIT cells in the barrier tissues. However, CD69 expression on tissue-associated MAIT cells was increased in AF mice compared to pair-fed (PF) mice. The expression of Th1 cytokines and the corresponding transcriptional factor was tissue specific with downregulation in the intestine, but increased in the lung and liver in alcohol-fed animals. Transplantation of fecal microbiota from AF mice resulted in a MAIT cell profile aligned to that of AF mice donor. Antibiotic treatment abolished the MAIT cell differences between AF and PF animals. Conclusion MAIT cells in the intestine, liver, and lung are perturbed by alcohol use, and these changes are, partially attributable to alcohol-associated dysbiosis. MAIT cell dysfunction may contribute to alcohol-induced, innate and adaptive immunity and consequently end-organ pathophysiology.

Private well water systems in rural areas that are improperly maintained will result in poor drinking water quality, loss of water supply, and pose human health risk. The purpose of this study was to investigate the occurrence of fecal indicator bacteria (FIB) and opportunistic pathogens in private well water in rural areas surrounding New Orleans, Louisiana. Our results confirmed the ubiquitous nature of Legionella (86.7%) and mycobacteria (68.1%) in private well water in the study area, with gene concentration ranged from 0.60 to 5.53 and 0.67 to 5.95 Log10 of GC/100 mL, respectively. Naegleria fowleri target sequence was detected in 16.8% and Escherichia coli was detected in 43.4% of the water samples. Total coliform, as well as Legionella and mycobacteria genetic markers' concentrations were significantly reduced by 3-minute flushing. Next-generation sequencing (NGS) data indicated that the abundance of bacterial species was significantly increased in water collected in kitchens compared with samples from wells directly. This study provided integrated knowledge on the persistence of pathogenic organisms in private well water. Further study is needed to explore the presence of clinical species of those opportunistic pathogens in private well water systems to elucidate the health risk.

Seagrass meadows in far South Texas are dominated by turtle grass (Thalassia testudinum), and juvenile pinfish (Lagodon rhomboides) are abundant grazers of seagrass epifauna. As they grow, pinfish exhibit an ontogenetic dietary shift and begin consuming increasing amounts of plant material. In this study, contrasting environmental regimes in two seagrass meadows were examined to identify how they might affect pinfish diets, diet shifts, and growth across the growing season. The eastern site was sheltered from prevailing southeasterly winds by a barrier island, while the western site was shallower and subjected to higher wind energy and turbidity. Gut contents from 290 pinfish were quantified from May through October 2016 and multivariate analyses showed strong but overlapping separation of diets and temporal change in feeding habits. Although there were spatial and temporal differences between the two sites, a site by time interaction indicated different temporal trends. Nonetheless, ooze (amorphous detritus) and aquatic invertebrates (primarily amphipods) were the primary diet items consumed at both localities across time. Pinfish at both sites consumed seagrass, which increased in importance as the growing season progressed, although volume and consumption rate did not differ between sites. Growth rates of pinfish were similar at both sites, but pinfish from the western site were larger and fewer in number across the study. Although pinfish diets differed under different environmental regimes, they were generalist consumers in South Texas seagrass meadows with high diet variability that trended towards herbivory in late summer and fall.

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

In vitro studies indicate IFNγ is central to Chlamydia trachomatis (Ct) eradication, but its function may be compromised by anaerobes typically associated with bacterial vaginosis (BV), a frequent co-morbidity in women with Ct. Here we investigated the associations between natural clearance of cervical Ct infection, the vaginal microbiome, and the requirements for IFNγ by evaluating the vaginal microbial and cytokine composition of Ct treatment visit samples from women who cleared Ct infection in the interim between their Ct screening and Ct treatment visit. The pilot cohort was young, predominantly African American, and characterized by a high rate of BV that was treated with metronidazole at the Ct screening visit. The rate of natural Ct clearance was 23.6% by the Ct treatment visit (median 9 days). 16S rRNA gene sequencing revealed that metronidazole-treated women who had a Lactobacillus spp.-dominant vaginal microbiota (CST 2 or 3) at the Ct treatment visit, were more prevalent in the Ct clearing population than the non-clearing population (86% v. 50%). L. iners (CST2) was the major Lactobacillus spp. present in Ct clearers, and 33% still remained anaerobe-dominant (CST1). Vaginal IFNγ levels were not significantly different in Ct clearers and non-clearers and were several logs lower than that required for killing Ct in vitro. An expanded panel of IFNγ-induced and proinflammatory cytokines and chemokines also did not reveal differences between Ct clearers and non-clearers, but, rather, suggested signatures better associated with specific CSTs. Taken together, these findings suggest that BV-associated bacteria may impede Ct clearance, but a Lactobacillus spp.-dominant microbiome is not an absolute requirement to clear. Further, IFNγ may be required at lower concentrations than in vitro modeling indicates, suggesting it may act together with other factors in vivo. Data also revealed that the vaginal bacteria-driven inflammation add complexity to the genital cytokine milieu, but changes in this microbiota may contribute to, or provide cytokine biomarkers, for a shift to Ct clearance.

Treg deficiency causes a lethal, CD4(+) T cell-driven autoimmune disease called IPEX syndrome (immunodysregulation, polyendocrinopathy, and enteropathy, with X-linked inheritance) in humans and in the scurfy (SF) mouse, a mouse model of the disease. Feeding Limosilactobacillus reuteri DSM 17938 (LR 17938, LR) to SF mice reprograms the gut microbiota, reduces disease progression, and prolongs lifespan. However, the efficacy and mechanism of LR, compared with other probiotics, in producing these effects is unknown. We compared LR with Lacticaseibacillus rhamnosus GG (LGG), an extensively investigated probiotic. LR was more effective than LGG in prolonging survival. Both probiotics restored the fecal microbial alpha diversity, but they produced distinct fecal bacterial clusters and differentially modulated microbial relative abundance (RA). LR increased the RA of phylum_Firmicutes, genus_Oscillospira whereas LR reduced phylum_Bacteroidetes, genus_Bacteroides and genus_Parabacteroides, reversing changes attributed to the SF phenotype. LGG primarily reduced the RA of genus_Bacteroides. Both LR and LGG reduced the potentially pathogenic taxon class_γ-proteobacteria. Plasma metabolomics revealed substantial differences among 696 metabolites. We observed similar changes of many clusters of metabolites in SF mice associated with treatment with either LR or LGG. However, a unique effect of LR was to increase the abundance of plasma adenosine metabolites such as inosine, which we previously showed had immune modulatory effects. In conclusion: 1) different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency; and 2) when comparing different probiotics, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that “one size does not fit all” in the treatment of autoimmune disease. NEW & NOTEWORTHY In the treatment of Treg-deficiency-induced autoimmunity, Limosilactobacillus reuteri DSM 17938 (LR) showed greater efficacy than Lacticaseibacillus rhamnosus GG (LGG). The study demonstrated that two different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency, but with many similarities in global plasma metabolites in general. However, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that “one size does not fit all” in the treatment of autoimmune disease.

Motivation We compiled a global database of long-term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones. Main types of variables contained The database includes 11,386 time-series of riverine fish community catch data, including 646,270 species-specific abundance records, together with metadata related to the geographical location and sampling methodology of each time-series. Spatial location and grain The database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins world-wide. Time period and grain The database encompasses the period 1951-2019. Each time-series is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years). Major taxa and level of measurement The database includes 944 species of ray-finned fishes (Class Actinopterygii). Software format csv. Main conclusion Our collective effort provides the most comprehensive long-term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm.

Background Inflammation persists among persons with human immunodeficiency virus (PWH) despite effective antiretroviral therapy and may contribute to T-cell dysfunction. Alcohol use is prevalent among PWH and promotes intestinal leak, dysbiosis, and a proinflammatory milieu. Whether alcohol use is associated with T-cell late differentiation remains to be investigated. Methods Data and samples from PWH (N = 359 of 365) enrolled in the New Orleans Alcohol Use in HIV Study were used. Alcohol use was assessed by self-report (Alcohol Use Disorders Identification Test; lifetime alcohol exposure; 30-day Alcohol Timeline Followback) and phosphatidylethanol (PEth) quantitation. In a subset of participants, fecal bacterial content was assessed by ribosomal 16S marker gene deep sequencing and quantitative polymerase chain reaction. Intestinal leak was assessed by fecal-to-plasma α-1-antitrypsin (A1AT) enzyme-linked immunosorbent assay ratio. Peripheral T-cell populations were quantified by flow cytometry. Results Alcohol Use Disorder Identification Test scores were positively associated with activated-senescent, exhausted, and terminal effector memory CD45RA+CD8+ but not CD4+ T cells (cells/μL) after confounder adjustment (P Conclusions Alcohol use among PWH is associated with CD8+ T-cell late differentiation, intestinal leak, and dysbiosis. Alcohol-associated dysbiosis is implicated in CD8+ T-cell senescence.

Background Nearly all corn seed in the US is coated with neonicotinoid insecticides to protect against soil and foliar arthropod pests. Exposure in the soil and the systemic activity in the plant can pose non-target risks. We assessed the community-level effects of clothianidin-treated seed on the diversity and abundance of arthropod communities in a no-till corn agroecosystem over a single growing season. Results Epigeal and foliage-dwelling communities were disturbed by the clothianidin seed treatment, with significant negative and positive changes in taxa abundances. Clothianidin reduced the abundance of minute pirate bugs by 66.2%, lady beetles by 44.7%, ants by 43.4%, ground beetle adults and larvae by 31.7%, and rove beetles by 44.1% during the early corn growth stages. Herbivores, particularly thrips, were more negatively affected by clothianidin than other trophic groups. In contrast, some groups, such as collembolans and leafhoppers, exhibited significantly higher abundances in the seed treated plots. Conclusion Clothianidin primarily influenced arthropod communities during the 4 weeks following planting, with disruptions to major natural enemy taxa, but communities showed trends toward recovery at the later corn stages. While the insecticide suppressed multiple herbivores, none were economically damaging to corn; thus, the pest suppression benefits of clothianidin observed in this study did not justify the non-target impacts. © 2018 Society of Chemical Industry.

Our recent studies have shown that BrpA in Streptococcus mutans plays a critical role in cell envelope biogenesis, stress responses, and biofilm formation. In this study, a 10-species consortium was used to assess how BrpA deficiency influences the establishment, persistence, and competitiveness of S. mutans during growth in a community under conditions typical of the oral cavity. Results showed that, like the wild-type, the brpA mutant was able to colonize and establish on the surfaces tested. Relative to the wild-type, however, the brpA mutant had a reduced ability to persist and grow in the 10-species consortium (P .001). A rat caries model was also used to examine the effect of BrpA, as well as Psr, a BrpA paralog, on S. mutans cariogenicity. The results showed no major differences in infectivity between the wild-type and the brpA and psr mutants. Unlike the wild-type, however, infection with the brpA mutant, but not the psr mutant, showed no significant differences in both total numbers of carious lesions and caries severity, compared with the control group that received bacterial growth medium (P .05). Metagenomic and quantitative polymerase chain reaction analysis showed that S. mutans infection caused major alterations in the composition of the rats' plaque microbiota and that significantly less S. mutans was identified in the rats infected with the brpA mutant compared with those infected with the wild-type and the psr mutant. These results further suggest that BrpA plays a critical role in S. mutans pathophysiology and that BrpA has potential as a therapeutic target in the modulation of S. mutans virulence.

Objective This study used CD obesity-prone (OP) and obesity-resistant (OR) rats to examine how weight gain and fat accretion relate to fermentation levels and microbiota composition after feeding resistant starch (RS). Methods After feeding OP rats and OR rats a high-fat (HF) diet for 4 weeks, rats were stratified into three groups: they were fed either an HF diet (group 1: HF-HF) or were switched to a low-fat (LF) diet (group 2: HF-LF) or an LF diet supplemented with 20% RS by weight for 4 weeks (group 3: HF-LFRS). Energy intake, body weight, fermentation variables, and microbiota composition were determined. Results In OP rats, RS elicited robust fermentation (increased cecal contents, short-chain fatty acids, and serum glucagon-like peptide 1). Total bacteria, species of the Bacteroidales family S24-7, and the archaean Methanobrevibacter smithii increased. The robust fermentation did not elicit higher weight or fat accretion when compared with that of control rats fed the same isocaloric diets (HF-LF ± RS). In OR rats, body weight and fat accretion were also not different between HF-LF ± RS diets, but RS elicited minimal changes in fermentation and microbiota composition. Conclusions Robust fermentation did not contribute to greater weight. Fermentation levels and changes in microbiota composition in response to dietary RS differed by obesity phenotype.

Laboratory colonies are necessary to conduct year-round research on the invasive brown marmorated stink bug, Halyomorpha halys (Stal), a severe agricultural and nuisance pest in the USA. When adults are collected in the fall to either start or supplement colonies, they require a period of cold storage before they resume sexual development and egg production. There is a lack of understanding of how to collect and store diapause-triggered adults in the laboratory. A series of experiments in 2013–2015 assessed survival and fecundity of stink bugs collected from different locations and stored under different temperatures and durations. We found that a minimum of 7 weeks is necessary to break diapause and that a substantial proportion of adults can survive when stored at constant 9 °C, even for periods longer than needed to terminate diapause. Adults survived significantly better at 6 and 9 °C than at 3 °C in storage for 7 weeks. Longer durations up to 34 weeks in storage reduced adult survival and significantly affected survival rates, timing of first egg laying, and overall fecundity. Location where adults were collected at overwintering sites in the fall had a significant impact on survival in cold storage and colony performance. Adults collected from soybean fields in mid-September and fed in the laboratory for 2 weeks before storage had lower survival than adults collected in October at aggregation sites and stored immediately. The food sources available to H. halys adults at collection locations for nutrition and sequestration of sufficient energy reserves going into diapause are discussed.

We have previously demonstrated promotion of diethylnitrosamine (DEN) initiated liver tumorigenesis after feeding diets high in fat or ethanol (EtOH) to male mice. This was accompanied by hepatic induction of the proto-oncogene PIKE (Agap2). Switch of dietary protein from casein to soy protein isolate (SPI) significantly reduced tumor formation in these models. We have linked EtOH consumption in mice to microbial dysbiosis. Adoptive transfer studies demonstrate that microbiota from mice fed ethanol can induce hepatic steatosis in the absence of ethanol suggesting that microbiota or the microbial metabolome play key roles in development of fatty liver disease. Feeding SPI significantly changed gut bacteria in mice increasing alpha diversity (P < 0.05) and levels of Clostidiales spp. Feeding soy formula to piglets also resulted in significant changes in microbiota, the pattern of bile acid metabolites and in inhibition of the intestinal-hepatic FXR/FGF19-SHP pathway which has been linked to both steatosis and hepatocyte proliferation. Moreover, feeding SPI also resulted in induction of hepatic PPARα signaling and inhibition of PIKE mRNA expression coincident with inhibition of steatosis and cancer prevention. Feeding studies in the DEN model with differing dietary fats demonstrated tumor promotion specific to the saturated fat, cocoa butter relative to diets containing olive oil or corn oil associated with microbial dysbiosis including dramatic increases in Lachnospiraceae particularly from the genus Coprococcus. Immunohistochemical analysis demonstrated that tumors from EtOH-fed mice and patients with alcohol-associated HCC also expressed high levels of a novel cytochrome P450 enzyme CYP2W1. Additional adoptive transfer experiments and studies in knockout mice are required to determine the exact relationship between soy effects on the microbiota, expression of PIKE, CYP2W1, PPARα activation and prevention of tumorigenesis.

Early administration of Lactobacillus reuteri DSM 17938 (LR) prevents necrotizing enterocolitis and inhibits regulatory T-cell (Treg)-deficiency-associated autoimmunity in mice. In humans, LR reduces crying time in breastfed infants with colic, modifies severity in infants with acute diarrheal illnesses, and improves pain in children with functional bowel disorders. In healthy breastfed newborns with evolving microbial colonization, it is unclear if early administration of LR can modulate gut microbiota and their metabolites in such a way as to promote homeostasis. We gavaged LR (107colony-forming units/day, daily) to C57BL/6J mice at age of day 8 for 2 wk. Both male and female mice were investigated in these experiments. We found that feeding LR did not affect clinical phenotype or inflammatory biomarkers in plasma and stool, but LR increased the proportion of Foxp3+regulatory T cells (Tregs) in the intestine. LR also increased bacterial diversity and the relative abundance of p_Firmicutes, f_Lachnospiraceae, f_Ruminococcaceae, and genera Clostridium and Candidatus arthromitus, while decreasing the relative abundance of p_Bacteriodetes, f_Bacteroidaceae, f_Verrucomicrobiaceae, and genera Bacteroides, Ruminococcus, Akkermansia, and Sutterella. Finally, LR exerted a major impact on the plasma metabolome, upregulating amino acid metabolites formed via the urea, tricarboxylic acid, and methionine cycles and increasing tryptophan metabolism. In conclusion, early oral administration of LR to healthy breastfed mice led to microbial and metabolic changes which could be beneficial to general health.NEW & NOTEWORTHY Oral administration of Lactobacillus reuteri DSM 17938 (LR) to healthy breastfed mice promotes intestinal immune tolerance and is linked to proliferation of beneficial gut microbiota. LR upregulates plasma metabolites that are involved in the urea cycle, the TCA cycle, methionine methylation, and the polyamine pathway. Herein, we show that LR given to newborn mice specifically increases levels of tryptophan metabolites and the purine nucleoside adenosine that are known to enhance tolerance to inflammatory stimuli.

Gram-negative bacteria of the human gastrointestinal (GI) tract microbiome: (i) are capable of generating a broad-spectrum of highly neurotoxic, pro-inflammatory and potentially pathogenic molecules; and (ii) these include a highly immunogenic class of amphipathic surface glycolipids known as lipopolysaccharide (LPS). Bacteroides fragilis (B. fragilis), a commensal, Gram negative, non-motile, non-spore forming obligatory anaerobic bacillus, and one of the most abundant bacteria found in the human GI tract, produces a particularly pro-inflammatory and neurotoxic LPS (BF-LPS). BF-LPS: (i) is known to be secreted from the B. fragilis outer membrane into the external-medium; (ii) can damage biophysiological barriers via cleavage of zonula adherens cell-cell adhesion proteins, thereby disrupting both the GI-tract barrier and the blood-brain barrier (BBB); (iii) is able to transit GI-tract barriers into the systemic circulation and cross the BBB into the human CNS; and (iv) accumulates within CNS neurons in neurodegenerative disorders such as Alzheimer’s disease (AD). This short communication provides evidence that the incubation of B. fragilis with aluminum sulfate [Al(2)(SO(4))(3)] is a potent inducer of BF-LPS. The results suggest for the first time that the pro-inflammatory properties of aluminum may not only be propagated by aluminum itself, but by a stimulation in the production of microbiome-derived BF-LPS and other pro-inflammatory pathogenic microbial products normally secreted from human GI-tract-resident microorganisms. GRAPHICAL ABSTRACT: Gram-negative bacteria such as B. fragilis of the human gastrointestinal (GI) tract microbiome generate pro-inflammatory glycolipids known as lipopolysaccharide (LPS) and other neurotoxic species, and are amongst the most pro-inflammatory molecules known. Incubation of aluminum sulfate [Al(2)(SO(4))(3)] with B. fragilis in culture resulted in a significant increase in the release of LPS.

Background Regulatory T cell (Treg) deficiency leads to IPEX syndrome, a lethal autoimmune disease, in Human and mice. Dysbiosis of the gut microbiota in Treg-deficient scurfy (SF) mice has been described, but to date, the role of the gut microbiota remains to be determined. Results To examine how antibiotic-modified microbiota can inhibit Treg deficiency-induced lethal inflammation in SF mice, Treg-deficient SF mice were treated with three different antibiotics. Different antibiotics resulted in distinct microbiota and metabolome changes and led to varied efficacy in prolonging lifespan and reducing inflammation in the liver and lung. Moreover, antibiotics altered plasma levels of several cytokines, especially IL-6. By analyzing gut microbiota and metabolome, we determined the microbial and metabolomic signatures which were associated with the antibiotics. Remarkably, antibiotic treatments restored the levels of several primary and secondary bile acids, which significantly reduced IL-6 expression in RAW macrophages in vitro. IL-6 blockade prolonged lifespan and inhibited inflammation in the liver and lung. By using IL-6 knockout mice, we further identified that IL-6 deletion provided a significant portion of the protection against inflammation induced by Treg dysfunction. Conclusion Our results show that three antibiotics differentially prolong survival and inhibit lethal inflammation in association with a microbiota—IL-6 axis. This pathway presents a potential avenue for treating Treg deficiency-mediated autoimmune disorders.

Bacterial vaginosis (BV) is the most common cause of vaginal discharge. It is associated with an increased risk of preterm delivery, pelvic inflammatory disease, and an increased risk of acquisition of sexually transmitted infections including human immunodeficiency virus (HIV). The epidemiology of BV supports sexual transmission. However, its etiology remains unknown. At the center of the debate is whether BV is caused by a primary pathogen or a polymicrobial consortium of microorganisms that are sexually transmitted. We previously published a conceptual model hypothesizing that BV is initiated by sexual transmission of Gardnerella vaginalis. Critics of this model have iterated that G. vaginalis is found in virginal women and in sexually active women with a normal vaginal microbiota. In addition, colonization does not always lead to BV. However, recent advances in BV pathogenesis research have determined the existence of 13 different species within the genus Gardnerella. It may be that healthy women are colonized by nonpathogenic Gardnerella species, whereas virulent strains are involved in BV development. Based on our results from a recent prospective study, in addition to an extensive literature review, we present an updated conceptual model for the pathogenesis of BV that centers on the roles of virulent strains of G. vaginalis, as well as Prevotella bivia and Atopobium vaginae., This work was supported by the National Institute of Allergy and Infectious Diseases (grant K23AI106957 to C. A. M.)., info:eu-repo/semantics/publishedVersion

He et al. show that T reg deficiency markedly induces autoimmunity and shifts gut microbiota. Remodeling microbiota by Lactobacillus reuteri was found to inhibit autoimmunity via the metabolite inosine, which interacts with the adenosine A2A receptor. This finding establishes a link between the gut microbiota, A2A receptors, and autoimmunity induced by T reg cell deficiency., Regulatory T (T reg) cell deficiency causes lethal, CD4+ T cell–driven autoimmune diseases. Stem cell transplantation is used to treat these diseases, but this procedure is limited by the availability of a suitable donor. The intestinal microbiota drives host immune homeostasis by regulating the differentiation and expansion of T reg, Th1, and Th2 cells. It is currently unclear if T reg cell deficiency–mediated autoimmune disorders can be treated by targeting the enteric microbiota. Here, we demonstrate that Foxp3+ T reg cell deficiency results in gut microbial dysbiosis and autoimmunity over the lifespan of scurfy (SF) mouse. Remodeling microbiota with Lactobacillus reuteri prolonged survival and reduced multiorgan inflammation in SF mice. L. reuteri changed the metabolomic profile disrupted by T reg cell deficiency, and a major effect was to restore levels of the purine metabolite inosine. Feeding inosine itself prolonged life and inhibited multiorgan inflammation by reducing Th1/Th2 cells and their associated cytokines. Mechanistically, the inhibition of inosine on the differentiation of Th1 and Th2 cells in vitro depended on adenosine A2A receptors, which were also required for the efficacy of inosine and of L. reuteri in vivo. These results reveal that the microbiota–inosine–A2A receptor axis might represent a potential avenue for combatting autoimmune diseases mediated by T reg cell dysfunction.

Pneumocystis pneumonia is a major cause of morbidity and mortality in patients infected with HIV/AIDS. In this study, we evaluated the intestinal microbial communities associated with the development of experimental Pneumocystis pneumonia, as there is growing evidence that the intestinal microbiota is critical for host defense against fungal pathogens.C57BL/6 mice were infected with live Pneumocystis murina (P. murina) via intratracheal inoculation and sacrificed 7 and 14 days postinfection for microbiota analysis. In addition, we evaluated the intestinal microbiota from CD4+ T cell depleted mice infected with P. murina.We found that the diversity of the intestinal microbial community was significantly altered by respiratory infection with P. murina. Specifically, mice infected with P. murina had altered microbial populations, as judged by changes in diversity metrics and relative taxa abundances. We also found that CD4+ T cell depleted mice infected with P. murina exhibited significantly altered intestinal microbiota that was distinct from immunocompetent mice infected with P. murina, suggesting that loss of CD4+ T cells may also affects the intestinal microbiota in the setting of Pneumocystis pneumonia. Finally, we employed a predictive metagenomics approach to evaluate various microbial features. We found that Pneumocystis pneumonia significantly alters the intestinal microbiota's inferred functional potential for carbohydrate, energy, and xenobiotic metabolism, as well as signal transduction pathways.Our study provides insight into specific-microbial clades and inferred microbial functional pathways associated with Pneumocystis pneumonia. Our data also suggest a role for the gut-lung axis in host defense in the lung.

The brown marmorated stink bug, Halyomorpha halys (Stal), is dependent on a beneficial obligate symbiont for successful development, survival, and fecundity. The bacteria are deposited on the egg mass surface by the female, and first instar nymphs become inoculated with the bacteria by feeding on the egg chorions upon hatching. Targeting the bacteria exposed on the egg mass surface may prove to be a viable management strategy for the stink bug. Egg masses were surface-treated with several antimicrobials and surfactants to determine whether exposure to these products adversely affected the fitness of newly hatched nymphs and/or sterilized the egg mass surface to prevent nymphal acquisition of the symbiont. Laboratory results showed that egg hatch rate was significantly reduced by Agri-Mycin and Naiad, nymphal survival was significantly impacted by AzaGuard and Naiad, and symbiont acquisition was significantly disrupted by Naiad, AzaGuard, and Liquid Copper Fungicide. Under field conditions, there were no significant treatment effects on nymphal survival or symbiont acquisition, but egg hatch rate was reduced by Naiad and Triton-X. Products with both antimicrobial effects and the ability to penetrate the coating covering the bacteria provided the best chance for disrupting symbiont acquisition.

Insect activity, survival, and development are affected by climatic conditions that elicit effects at multiple scales. Pruning small fruit crop canopies alters the microclimate, which in turn may influence insect pest activity. We investigated the effect of three canopy density treatments (high, medium, low) on Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) fruit infestation in blueberries and caneberries using a two-year, multi-state experiment. We quantified the effect of canopy density on canopy microclimate, fruit quality (total soluble solids, fruit firmness), and yield. To better understand heterogeneity in canopy microclimate, parameters were further separated by canopy location (exterior vs. interior) in Maryland. In both crops, meta-analyses reveal small magnitude effects of the plant canopy on microclimate, whereas analysis of variance did not separate these effects, with mean canopy differences of 0.1–0.7 °C and 0.5–1.3 % relative humidity (RH) between caneberry canopy densities and locations. In caneberry multi-state trials, 0.14 fewer D. suzukii larvae (g fruit)−1 occurred on average in the low canopy density treatment, and 0.2 fewer D. suzukii larvae (g fruit)−1 occurred in exterior raspberries in Maryland compared with the canopy interior. Artificially infested blueberry fruit indicated immature D. suzukii survival within fruit can vary across canopy densities and locations. Although lower total yield was produced in low density canopies, canopy density did not influence berry quality or marketable yield. Microhabitats provide important shelter from extreme environmental conditions; the availability of shelter and ability to locate it affects insect pest populations and distributions. Understanding how crop canopy microclimate affects D. suzukii infestation can inform efforts to develop habitat manipulation tactics and improve the efficiency of fruit production.

Background Fruit growers largely depend on chemical control to reduce populations of the economically damaging invasive fly, Drosophila suzukii (Matsumura). Drosophila suzukii is susceptible to high temperatures and low humidity; therefore, it may be possible to implement cultural control practices that create microclimates unfavorable for its development and survival. In addition to other fruit production benefits, in-row mulches may impede the development of D. suzukii immatures when larvae leave the fruit to pupate in the soil. This study compared the effects of different mulches (black polypropylene fabric weedmats, sawdust, and wood chips) on temperature and relative humidity (RH), and on adult emergence of D. suzukii from larvae in blueberries and pupae, both above and below the ground surface in blueberry plantings (Vaccinium corymbosum L.). Results Across regions, both lower larval survival and longer periods with high suboptimal temperatures occurred above the ground in comparison to buried below the ground, regardless of mulch type. Fewer D. suzukii adults emerged from larvae on weedmat mulch at one site, but there was no effect of mulch type on temperature, RH, or D. suzukii emergence at most sites. The relationships between temperature, RH, and the emergence of adults from larvae and pupae varied by region. Natural infestation by D. suzukii in blueberries was lower over weedmat compared to wood-based mulches at one site. Greenhouse experiments showed that larvae burrowed to pupate underneath sawdust mulch, but were unable to pupate underneath a weedmat mulch. Conclusions Although weedmats may not modify temperatures or RH enough to consistently affect D. suzukii emergence, they can reduce field suitability for D. suzukii by providing a barrier that prevents larvae from reaching favorable pupation microhabitats underground. © 2019 Society of Chemical Industry.

OBJECTIVE: To dissect potential confounding effects of breast milk and formula feeding on crying + fussing, fecal calprotectin, and gut microbiota in babies with colic. We hypothesized that infant colic is associated with gut inflammation linked to intestinal dysbiosis. STUDY DESIGN: A nested case-control design of 3 of our studies was used to analyze clinical and laboratory data at presentation, comparing babies with colic with controls. All investigators other than the biostatistician were blinded during data analysis. Subjects were recruited based on their age and crying + fussy time. We screened 65 infants, 37 with colic, as defined by Barr diary (crying + fussing time >3 hours daily), who were compared with 28 noncolicky infants. RESULTS: Fecal calprotectin was elevated in babies with colic. For each mode of infant feeding (breast milk, formula, or breast + formula), infants’ fecal calprotectin was higher in babies with colic. Infants with colic had similar levels of fecal alpha diversity (richness) when compared with controls, and alpha diversity was lower in breast-fed babies. Beta diversity at the phylum level revealed significant differences in microbial population. A phylum difference resulted from reduced Actinobacteria (95% of which are Bifidobacilli) in babies with colic. Species significantly associated with colic were Acinetobacter and Lactobacillus iners. CONCLUSIONS: Colic is linked with gut inflammation (as determined by fecal calprotectin) and dysbiosis, independent of mode of feeding, with fewer Bifidobacilli. (J Pediatr 2018;203:55–61). TRIAL REGISTRATION: Clinicaltrials.gov: https://register.clinicaltrials.gov/ and https://register.clinicaltrials.gov/.

Alcohol use in persons living with HIV (PLWH) worsens the severity of bacterial pneumonia. However, the exact mechanism(s) by which this occurs remain ill-defined. We hypothesized that alcohol in the setting of HIV infection decreases Streptococcus pneumoniae clearance from the lung through mechanisms mediated by the gut microbiota. Humanized BLT (bone marrow, liver, thymus) mice were infected with 1 × 104 TCID50 of HIV (BAL and JRCSF strains) via intraperitoneal (i.p.) injection. One week post-HIV infection, animals were switched to a Lieber-DeCarli 5% ethanol diet or an isocaloric control diet for 10 days. Alcohol-fed animals were also given two binges of 2 g/kg ethanol on days 5 and 10. Feces were also collected, banked, and the community structures were analyzed. Mice were then infected with 1 × 105 CFU (colony-forming units) of S. pneumoniae and were sacrificed 48 h later. HIV-infected mice had viral loads of ∼2 × 104 copies/mL of blood 1 week post-infection, and exhibited an ∼57% decrease in the number of circulating CD4+ T cells at the time of sacrifice. Fecal microbial community structure was significantly different in each of the feeding groups, as well as with HIV infection. Alcohol-fed mice had a significantly higher burden of S. pneumoniae 48 h post-infection, regardless of HIV status. In follow-up experiments, female C57BL/6 mice were treated with a cocktail of antibiotics daily for 2 weeks and recolonized by gavage with intestinal microbiota from HIV+ ethanol-fed, HIV+ pair-fed, HIV− ethanol-fed, or HIV− pair-fed mice. Recolonized mice were then infected with S. pneumoniae and were sacrificed 48 h later. The intestinal microbiota from alcohol-fed mice (regardless of HIV status) significantly impaired clearance of S. pneumoniae. Collectively, these data indicate that alcohol feeding, as well as alcohol-associated intestinal dysbiosis, compromise pulmonary host defenses against pneumococcal pneumonia. Determining whether HIV infection acts synergistically with alcohol use in impairing pulmonary host defenses will require additional study.

Background The sequence of events preceding incident bacterial vaginosis (iBV) is unclear. Methods African American women who have sex with women, who had no Amsel criteria and Nugent scores of 0-3, were followed for 90 days to detect iBV (defined as a Nugent score of 7-10 on at least 2-3 consecutive days), using self-collected vaginal swab specimens. For women with iBV (cases) and women maintaining normal vaginal flora (healthy women), 16S ribosomal RNA gene sequencing targeting V4 was performed. Longitudinal vaginal microbiome data were analyzed. Results Of 204 women screened, 42 enrolled; of these, 45% developed iBV. Sequencing was performed on 448 specimens from 14 cases and 8 healthy women. Among healthy women, Lactobacillus crispatus dominated the vaginal microbiota in 75%. In contrast, prior to iBV, the vaginal microbiota in 79% of cases was dominated by Lactobacillus iners and/or Lactobacillus jensenii/Lactobacillus gasseri. The mean relative abundance of Prevotella bivia, Gardnerella vaginalis, Atopobium vaginae, and Megasphaera type I became significantly higher in cases 4 days before (P. bivia), 3 days before (G. vaginalis), and on the day of (A. vaginae and Megasphaera type I) iBV onset. The mean relative abundance of Sneathia sanguinegens, Finegoldia magna, BV-associated bacteria 1-3, and L. iners was not significantly different between groups before onset of iBV. Conclusion G. vaginalis, P. bivia, A. vaginae, and Megasphaera type I may play significant roles in iBV.

Pneumocystis pneumonia is a major cause of morbidity and mortality in immunocompromised patients, particularly those infected with HIV. In this study, we evaluated the potential of oral immunization with live Pneumocystis to elicit protection against respiratory infection with Pneumocystis murina. C57BL/6 mice vaccinated with live P. murina using a prime-boost vaccination strategy were protected from a subsequent lung challenge with P. murina at 2, 7, 14, and 28 d postinfection even after CD4+ T cell depletion. Specifically, vaccinated immunocompetent mice had significantly faster clearance than unvaccinated immunocompetent mice and unvaccinated CD4-depleted mice remained persistently infected with P. murina. Vaccination also increased numbers of CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD11b+ macrophages in the lungs following respiratory infection. In addition, levels of lung, serum, and fecal P. murina–specific IgG and IgA were increased in vaccinated animals. Furthermore, administration of serum from vaccinated mice significantly reduced Pneumocystis lung burden in infected animals compared with control serum. We also found that the diversity of the intestinal microbial community was altered by oral immunization with P. murina. To our knowledge, our data demonstrate for the first time that an oral vaccination strategy prevents Pneumocystis infection.

Walnuts are rich in omega-3 fatty acids, phytochemicals and antioxidants making them unique compared to other foods. Consuming walnuts has been associated with health benefits including a reduced risk of heart disease and cancer. Dysbiosis of the gut microbiome has been linked to several chronic diseases. One potential mechanism by which walnuts may exert their health benefit is through modifying the gut microbiome. This study identified the changes in the gut microbial communities that occur following the inclusion of walnuts in the diet. Male Fischer 344 rats (n=20) were randomly assigned to one of two diets for as long as 10 weeks: (1) walnut (W), and (2) replacement (R) in which the fat, fiber, and protein in walnuts were matched with corn oil, protein casein, and a cellulose fiber source. Intestinal samples were collected from the descending colon, the DNA isolated, and the V3-V4 hypervariable region of 16S rRNA gene deep sequenced on an Illumina MiSeq for characterization of the gut microbiota. Body weight and food intake did not differ significantly between the two diet groups. The diet groups had distinct microbial communities with animals consuming walnuts displaying significantly greater species diversity. Walnuts increased the abundance of Firmicutes and reduced the abundance of Bacteriodetes. Walnuts enriched the microbiota for probiotic-type bacteria including Lactobacillus, Ruminococcaceae, and Roseburia while significantly reducing Bacteroides and Anaerotruncus. The class Alphaproteobacteria was also reduced. Walnut consumption altered the gut microbial community suggesting a new mechanism by which walnuts may confer their beneficial health effects. (C) 2017 The Authors. Published by Elsevier Inc. American Institute for Cancer Research; California Walnut Commission This work was supported by the American Institute for Cancer Research and California Walnut Commission.

Chronic alcohol consumption perturbs the normal intestinal microbial communities (dysbiosis). To investigate the relationship between alcohol-mediated dysbiosis and pulmonary host defense we developed a fecal adoptive transfer model, which allows us to investigate the impact of alcohol-induced gut dysbiosis on host immune response to an infectious challenge at a distal organ, independent of prevailing alcohol use. Male C57BL/6 mice were treated with a cocktail of antibiotics (ampicillin, gentamicin, neomycin, vancomycin, and metronidazole) via daily gavage for two weeks. A separate group of animals was fed a chronic alcohol (or isocaloric dextrose pair-fed controls) liquid diet for 10 days. Microbiota-depleted mice were recolonized with intestinal microbiota from alcohol-fed or pair-fed (control) animals. Following recolonization groups of mice were sacrificed prior to and 48 hrs. post respiratory infection with Klebsiella pneumoniae. Klebsiella lung burden, lung immunology and inflammation, as well as intestinal immunology, inflammation, and barrier damage were examined. Results showed that alcohol-associated susceptibility to K. pneumoniae is, in part, mediated by gut dysbiosis, as alcohol-naïve animals recolonized with a microbiota isolated from alcohol-fed mice had an increased respiratory burden of K. pneumoniae compared to mice recolonized with a control microbiota. The increased susceptibility in alcohol-dysbiosis recolonized animals was associated with an increase in pulmonary inflammatory cytokines, and a decrease in the number of CD4+ and CD8+ T-cells in the lung following Klebsiella infection but an increase in T-cell counts in the intestinal tract following Klebsiella infection, suggesting intestinal T-cell sequestration as a factor in impaired lung host defense. Mice recolonized with an alcohol-dysbiotic microbiota also had increased intestinal damage as measured by increased levels of serum intestinal fatty acid binding protein. Collectively, these results suggest that alterations in the intestinal immune response as a consequence of alcohol-induced dysbiosis contribute to increased host susceptibility to Klebsiella pneumonia., Author summary Alcohol use disorders (AUD) are an established risk factor for bacterial pneumonia. Further, alcohol consumption perturbs the normal intestinal microbial communities. Intestinal microbiota dysbiosis has been linked to impaired pulmonary host defense, however the role of alcohol-associated intestinal dysbiosis on pulmonary host defense is unknown. Here, we used an innovative model system to examine the role of alcohol-mediated intestinal dysbiosis on pulmonary host defense against respiratory infection with Klebsiella pneumoniae, independent of direct alcohol toxicity. We found that alcohol-mediated dysbiosis significantly increases host susceptibility to K. pneumoniae infection, independent of prevailing alcohol consumption. Alcohol-dysbiosis was associated with an altered T-cell responses in both the lung and intestinal tract following Klebsiella infection. Alcohol-dysbiosis also lead to increased pulmonary inflammation, as well as intestinal inflammation and damage. Our study demonstrates that alcohol-mediated dysbiosis impacts host defense and contributes to the impaired host defense against pneumonia frequently seen in alcohol abusers, and thus shifts conventional understanding of mechanisms of host defense impacted by alcohol. Characterization of microbial populations and metabolic products that regulate the immune system during harmful alcohol use may reveal novel therapeutic targets, as well as host-specific microbial communities that may be central to alcohol-mediated alterations in host defense.

The gut microbiome plays an important role in immune function and has been implicated in multiple sclerosis (MS). However, how to modulate microbiota to prevent or treat MS remain largely unknown. Probiotic Lactobacillus reuteri DSM 17938 (L. reuteri) has anti-inflammatory effects in mouse models of neonatal necrotizing enterocolitis and Treg-deficiency-induced autoimmune disease. L. reuteri in these models modulated gut microbiota and microbiota-associated metabolites to inhibit TH1 and TH2 differentiation and their-associated cytokines, significantly ameliorating the severity of these diseases. An in vitro study indicated that L. reuteri inhibits the differentiation of naïve CD4+T cells into TH17 and TH1 cells. We determined the effect of L. reuteri on experimental autoimmune encephalomyelitis (EAE) mouse model, a widely used animal model of MS, a model which is primarily mediated by TH17 and TH1 cells. We discovered that L. reuteri treatment reduced TH1/TH17 cells and their associated cytokines IFN-γ/IL-17 in EAE, inhibiting the development of EAE. We also showed that the loss of diversity in gut microbiota induced by EAE was largely restored by L. reuteri treatment. Taxonomy-based analysis of gut microbiota showed that the “beneficial” genera Bifidobacterium, Prevotella, and Lactobacillus were negatively correlated with EAE clinical severity scores, whereas the genera Anaeroplasma, Rikenellaceae, and Clostridium were positively correlated. Notably, L. reuteri treatment altered the relative abundances of these EAE-associated taxa in mice. In conclusion, probiotic L. reuteri changed gut microbiota to modulate immune responses in EAE, making it a novel candidate in future studies to modify the severity of MS.

The Rio Grande and its tributaries in the Trans-Pecos region of Texas have been impacted by a variety of anthropogenic activities such as dewatering and the introduction of nonnative species. These environmental manipulations have negatively affected the native fishes leading to extirpations and declining populations throughout the region. Campostoma ornatum and Notropis chihuahua inhabit tributary streams of the Rio Grande in the Trans-Pecos region and are considered as state-listed threatened species. Little is known about their status and ecological requirements in the region. We hypothesized that the distribution and abundance of these threatened minnows in these spring-fed habitats can be modeled by two primary factors: local environmental conditions that are maintained by spring flow and the abundance of introduced species such as the plains killifish, Fundulus zebrinus. We used classification and regression trees to analyze variation in abundance and incidence of the target species from Al...

Objective To assess the safety of probiotic Lactobacillus reuteri strain Deutsche Sammlung von Mikroorganismen (DSM) 17938 with daily administration to healthy infants with colic and to determine the effect of L reuteri strain DSM 17938 on crying, fussing, inflammatory, immune, and microbiome variables. Study design We performed a controlled, double-blinded, phase 1 safety and tolerability trial in healthy breast-fed infants with colic, aged 3 weeks to 3 months, randomly assigned to L reuteri strain DSM 17938 (5 × 108 colony-forming units daily) or placebo for 42 days and followed for 134 days. Results Of 117 screened infants, 20 were randomized to L reuteri strain DSM 17938 or placebo (sunflower oil) (in a 2:1 ratio) with 80% retention. Eleven of the 20 (55%) presented with low absolute neutrophil counts ( Conclusions Daily administration of L reuteri strain DSM 17938 appears to be safe in newborn infants with colic, including those with neutropenia, which frequently coexists. A placebo response of 66% suggests that many infants with colic will have resolution within 3 weeks. Trial registration ClinicalTrials.gov : NCT01849991 .

– The ashy darter, Etheostoma cinereum, is an imperiled fish within the Cumberland and Tennessee drainages of the southeast United States. An understanding of habitat associations and the relationship of habitat use across multiple spatial scales are critical elements in its conservation. Our objectives were to quantify habitat associations at the stream reach and microhabitat scales for adult and juvenile darters, and to understand the linkage between the two scales based on gradients of habitat use. We focused our efforts within the Rockcastle River, Kentucky (Cumberland River drainage), because the watershed was known to contain a relatively large ashy darter population. Three hundred twenty-two individuals were collected from 21 reaches. The species was restricted to the mainstem of the river and the lower reaches of the larger tributaries. The distribution and abundance of adult and juvenile darters differed significantly at each spatial scale, and both groups demonstrated non-random use of the available habitat. Gradients of stream size and substrate size were identified as important factors. A threshold of environmental quality was determined based on the habitat use patterns among the two scales. Habitat use between the two scales was independent within the threshold, indicating that the specific quality of the microhabitats did not necessarily matter within a stream reach. However, beyond the threshold, a decrease of at least 48% in adult and juvenile darter abundance was seen, indicating that a sufficient network of suitable microhabitats is needed to support a good population of darters within a stream reach.

The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity. Specific microbial genera were differentially abundant in the lower, middle, and upper 33rd percentiles of biological age. Using Sparse Inverse Covariance Estimation for Ecological Association and Statistical Inference (SPIEC-EASI) and Weighted Gene Co-Expression Network Analysis (WGCNA), we identified modules of coabundant microbial genera that distinguished biological from chronological aging. A biological age-associated module composed of Eggerthella, Ruminococcus, and Coprobacillus genera was robust to correction for subject age, sex, body mass index, antibiotic usage, and other confounders. Subject FI34 score positively correlated with the abundance of this module, which exhibited a distinct inferred metagenome as predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). We conclude that increasing biological age in community-dwelling adults is associated with gastrointestinal dysbiosis.

cope To determine if whole-grain (WG) flour with resistant starch (RS) will produce greater fermentation than isolated RS in obese Zucker Diabetic Fatty (ZDF) rats, and whether greater fermentation results in different microbiota, reduced abdominal fat, and increased insulin sensitivity. Methods and results This study utilized four groups fed diets made with either isolated digestible control starch, WG control flour (6.9% RS), isolated RS-rich corn starch (25% RS), or WG corn flour (25% RS). ZDF rats fermented RS and RS-rich WG flour to greatest extent among groups. High-RS groups had increased serum glucagon-like peptide 1 (GLP-1) active. Feeding isolated RS showed greater Bacteroidetes to Firmicutes phyla among groups, and rats consuming low RS diets possessed more bacteria in Lactobacillus genus. However, no differences in abdominal fat were observed, but rats with isolated RS had greatest insulin sensitivity among groups. Conclusions Data demonstrated ZDF rats (i) possess a microbiota that fermented RS, and (ii) WG high-RS fermented better than purified RS. However, fermentation and microbiota changes did not translate into reduced abdominal fat. The defective leptin receptor may limit ZDF rats from responding to increased GLP-1 and different microbiota for reducing abdominal fat, but did not prevent improved insulin sensitivity.

Next generation sequencing (NGS) can globally interrogate the genetic composition of biological samples in an unbiased yet sensitive manner. The objective of this study was to utilize the capabilities of NGS to investigate the reported association between glioblastoma multiforme (GBM) and human cytomegalovirus (HCMV). A large-scale comprehensive virome assessment was performed on publicly available sequencing datasets from the Cancer Genome Atlas (TCGA), including RNA-seq datasets from primary GBM (n = 157), recurrent GBM (n = 13), low-grade gliomas (n = 514), recurrent low-grade gliomas (n = 17), and normal brain (n = 5), and whole genome sequencing (WGS) datasets from primary GBM (n = 51), recurrent GBM (n = 10), and normal matched blood samples (n = 20). In addition, RNA-seq datasets from MRI-guided biopsies (n = 92) and glioma stem-like cell cultures (n = 9) were analyzed. Sixty-four DNA-seq datasets from 11 meningiomas and their corresponding blood control samples were also analyzed. Finally, three primary GBM tissue samples were obtained, sequenced using RNA-seq, and analyzed. After in-depth analysis, the most robust virus findings were the detection of papillomavirus (HPV) and hepatitis B reads in the occasional LGG sample (4 samples and 1 sample, respectively). In addition, low numbers of virus reads were detected in several datasets but detailed investigation of these reads suggest that these findings likely represent artifacts or non-pathological infections. For example, all of the sporadic low level HCMV reads were found to map to the immediate early promoter intimating that they likely originated from laboratory expression vector contamination. Despite the detection of low numbers of Epstein-Barr virus reads in some samples, these likely originated from infiltrating B-cells. Finally, human herpesvirus 6 and 7 aligned viral reads were identified in all DNA-seq and a few RNA-seq datasets but detailed analysis demonstrated that these were likely derived from the homologous human telomeric-like repeats. Other low abundance viral reads were detected in some samples but for most viruses, the reads likely represent artifacts or incidental infections. This analysis argues against associations between most known viruses and GBM or mengiomas. Nevertheless, there may be a low percentage association between HPV and/or hepatitis B and LGGs. Electronic supplementary material The online version of this article (doi:10.1186/s40478-016-0338-z) contains supplementary material, which is available to authorized users.

The Mississippi silverside (Menidia audens), now common throughout the Tennessee-Tombigbee Waterway (TTW) in Mississippi, apparently invaded this highly modified system from the Tennessee River, concurrent with TTW construction (1972–1985). Subsequent decline in distribution and abundance of the native brook silverside (Labidesthes sicculus) led to speculation that dietary competition with M. audens might be occurring. Therefore, diet data from sympatric and allopatric collections of the two silversides at several sites in TTW were analyzed using multivariate statistics and null models to test for significant dietary differences, overlap and niche shifts potentially attributable to habitat alteration. Diet overlap between the two silversides at sites of co-occurrence was greater than expected under the null model. Moreover, intraspecific food habits did not differ between individuals occurring in sympatry and those occurring in allopatry for either silverside. Thus, significant portions of their ...

The Bayou Darter, Etheostoma rubrum, is endemic to the Bayou Pierre system of southwestern Mississippi where it occupies swift, shallow riffles with coarse, firm substrata. The Bayou Pierre system has experienced extensive erosion in response to rapid headcutting leading to loss of riffle habitat and degradation of riverine conditions. Due to its high degree of habitat specificity along with ongoing habitat fragmentation and potentially reduced gene flow between isolated populations, the Bayou Darter is vulnerable to severe population declines and possible extinction. Our objectives were to quantify levels of genetic diversity in the mitochondrial control region and infer population structure across the range of the species. Sequencing of 106 sampled individuals revealed only three mtDNA haplotypes with one variable site. Haplotype diversity and nucleotide diversity were low (h ≤ 0.11 and π < 0.001), and there was no structure revealed among the four sampled populations. The low genetic diversity...

Non-parametric, multivariate analyses commonly used to characterize spatial and temporal patterns in the taxonomic composition of ecological communities can likewise be useful when applied to data generated from the examination of gut contents. A suite of analyses including non-metric multidimensional scaling (NMS), multi-response permutation procedures (MRPP), and indicator species analysis (ISA) revealed interesting dietary shifts that occurred across individuals of emerald shiner (Notropis atherirtoides) collected from among different habitats and two different time periods (preand post-impoundment of the upper Tombigbee River). These patterns were delineated from data that exhibited non-linear distribution and that incorporated measurements made at different scales, two factors that confound traditional parametric analyses. NMS ordination provided clear, graphic representation of the separation that occurred when N. atherinoides diets were viewed across space and time. MRPP analysis validated that the observed separation was statistically significant, and ISA complemented these other two analyses by identifying diet contributors that were indicative of each grouping.

The upper Tombigbee River in northeastern Mississippi now exists as a fragment, confluencing with and fed by an extensively modified aquatic landscape now called the Tennessee-Tombigbee Waterway (TTW). We examined the changes to fish assemblages and flow regime after waterway construction based on contemporary comparisons to historical fish collections and discharge data. The river’s flow regime has changed markedly since TTW construction. Analysis of discharge data from two stations for 15 years, pre- and post-waterway, indicated significant differences in flow regime including increased minimum and base flows, lower spring and higher late summer-autumn flows, and lower high flow durations, post-TTW. These changes corresponded to significantly reduced regional and local species richness, and strong shifts in fish assemblage structure across a 20 yr time span. Post-waterway fish assemblages were related strongly to measured environmental variables characterizing local habitats. Several lentic-adapted species increased their abundances in lower reaches of the river, including a recent invader to the TTW system, the Mississippi silverside Menidia audens. Fragmentation of river ecosystems via disruption to hydrologic regimes is a major threat to aquatic biodiversity worldwide. Because the flow regime of this fragmented river is in part controlled by waterway operations via five minimum flow control structures, adaptive conservation and management efforts could be implemented in order to maintain and potentially restore the natural flow regime and the ecological integrity of the system.

We sampled fishes and aquatic insects monthly (Jun.–Sept. 2002) from intermittent tributaries of the Alum Fork of the Saline River (Arkansas, U.S.A.) to quantify the response of fish and aquatic insect assemblage properties to seasonal desiccation and habitat fragmentation. We collected a total of 4219 individuals, representing 18 species of fishes and 27 families of aquatic insects. Changes in the composition of fish assemblages were significantly related to temporal variability in pool volume and location in the watershed. Smaller, upstream pools varied in volume more than downstream pools. Fish assemblages were significantly more similar through summer in downstream, larger pool habitats. Changes in the composition of aquatic insect families were related to variation in water quality conditions. Highly eutrophied sites were typically dominated by midge larvae (Chironomidae), resulting in highly similar assemblages over time. Our results support findings at larger space and time scales and call...

Los Terreros Creek, a reservoir-fragmented tributary in the upper Lerma River system of central Mexico, was sampled at four localities in wet (2001) and dry (2002) seasons to evaluate spatial and temporal patterns of fish assemblages, the conservation status of native fishes, and prevalence of exotic species. Two of five species present were non-native; the common carp (Cyprinus carpio) and the shortfin silverside (Chirostoma humboldtianum). Fish assemblages formed a strong gradient largely separating the lentic, reservoir-impacted, locality (downstream-most site) from the remaining lotic sites. The two most-upstream sites were not distinguishable based on structure of fish assemblages. Three of five species showed significant spatial variation in abundance. The Aztec shiner (Aztecula sallaei) occurred only at the lotic sites and the two species of silversides (Chirostoma) occurred only at the lentic site. Temporal trends in assemblages were less evident, but assemblages in the dry season had low...

We tested the hypothesis that predator experience and immediate predation threat would influence mating behaviors in male western mosquitofish (Gambusia affinis). A series of trials were conducted in which individual males with and without predator experience were placed in an aquarium with females. For each group of males, one Lepomis cyanellus was added as a predator in one-half of the trials. The results indicated that under immediate predation threat nauve males performed more copulatory attempts than those with predator experience. Naive males also tended to be smaller and attempted more chasing behaviors than predator-experienced males.

The effects of population density, fish density, and dissolved oxygen on body condition of late-instar nymphs of Stenonema tripunctatum (Ephemeroptera, Heptageniidae) were investigated using nymphs sampled from isolated, upland stream pools over summer in central Arkansas, USA. All three factors exhibited high variation among pools. Body condition was negatively related to fish density, and positively related to dissolved oxygen (when included in the model). High fish densities may be related to low body condition because they cause reduced foraging or force earlier emergence at small body sizes. These results emphasize the combined effects of biotic and abiotic factors on body condition in mayflies, and support earlier findings that population density is a less-important factor.

Background Necrotizing enterocolitis (NEC) is a devastating neonatal gastrointestinal disease that primarily affects premature infants. It is characterized by bowel inflammation and necrosis. In spite of extensive research, there has been little progress in decreasing the incidence or mortality of NEC over the past three decades. The exact etiology of NEC has not been identified. However, it is believed to result from an inappropriate immune response to gut microbiota. Using 454-pyrosequencing analyses of 16S rRNA genes that were PCR-amplified from stool DNA specimens, we compared the gut microbiota of infants with NEC to matched controls without NEC. The infants with NEC were then categorized into three subgroups based on severity: mild, severe, and lethal. We compared the microbiota among these subgroups and between each severity group and appropriate controls. Results Bacterial diversity and the relative abundance of Actinobacteria and Clostridia were significantly lower in NEC specimens compared to controls. The absence of Clostridia was significantly associated with NEC. Microbial diversity and Clostridia abundance and prevalence decreased with increasing severity of NEC. Conclusions Low bacterial diversity in stool specimens may be indicative of NEC and the severity of NEC. The low bacterial diversity, and the lack of Clostridia in lethal specimens, could indicate that the presence of a diverse bacterial population in the gut as well as the presence of taxa such as Clostridia may play a role in attenuating inflammation leading to NEC. Electronic supplementary material The online version of this article (doi:10.1186/s40168-015-0075-8) contains supplementary material, which is available to authorized users.

Background The prevalence of mental illness, particularly depression and dementia, is increased by obesity. Here, we test the hypothesis that obesity-associated changes in gut microbiota are intrinsically able to impair neurocognitive behavior in mice. Methods Conventionally housed, nonobese, adult male C57BL/6 mice maintained on a normal chow diet were subjected to a microbiome depletion/transplantation paradigm using microbiota isolated from donors on either a high-fat diet (HFD) or control diet. Following re-colonization, mice were subjected to comprehensive behavioral and biochemical analyses. Results The mice given HFD microbiota had significant and selective disruptions in exploratory, cognitive, and stereotypical behavior compared with mice with control diet microbiota in the absence of significant differences in body weight. Sequencing-based phylogenetic analysis confirmed the presence of distinct core microbiota between groups, with alterations in α- and β-diversity, modulation in taxonomic distribution, and statistically significant alterations to metabolically active taxa. HFD microbiota also disrupted markers of intestinal barrier function, increased circulating endotoxin, and increased lymphocyte expression of ionized calcium-binding adapter molecule 1, toll-like receptor 2, and toll-like receptor 4. Finally, evaluation of brain homogenates revealed that HFD-shaped microbiota increased neuroinflammation and disrupted cerebrovascular homeostasis. Conclusions Collectively, these data reinforce the link between gut dysbiosis and neurologic dysfunction and suggest that dietary and/or pharmacologic manipulation of gut microbiota could attenuate the neurologic complications of obesity.

fish assemblages each significantly accounted for the regional variation in mussel assemblages. Furthermore, mussel assemblages showed strong spatial autocorrelation. Variation partitioning revealed that pure fish effects accounted for 15.4% of the variation in mussel assemblages; pure spatial and environmental effects accounted for 16.1% and 7.8%, respectively. Shared variation among fish, space and environmental variables totaled 40%. Of this shared variation, 36.8% was associated with the fish matrix. Thus, the variation in mussel assemblages that was associated with the distribution and abundance of fishes was substantial (> 50%), indicating that fish community structure is an important determinant of mussel community structure. Although animals commonly disperse plants and, thus, influence the structure of plant communities, our results show a strong macroecological association between two disparate animal groups with one strongly affecting the assemblage structure of

One major factor leading to the imperilment of freshwater mussels (Bivalvia, Unionidae) has been the large-scale impoundment of rivers. We examined the distribution and abundance of mussels at 37 sites along a 240-km length of the Little River in southeastern Oklahoma, U.S.A., which is affected by both main- stem and tributary reservoirs. We observed a mussel extinction gradient downstream from impoundments in this river: with increasing distance from the mainstem reservoir there was a gradual, linear increase in mus- sel species richness and abundance. Mussel species distributions were significantly nested, with only sites fur- thest from the impoundment containing relatively rare species. Below the confluence with the inflow from the second reservoir these same trends were apparent but much weaker, and overall mussel abundance was greatly reduced. Our results suggest that considerable stream lengths are necessary to overcome the effects of impoundment on mussel populations, and such information should be considered in conservation and man- agement plans.