Effect of Bifidobacterium animalis spp. lactis Bl-04 on Rhinovirus-Induced Colds: A Randomized, Placebo-Controlled, Single-Center, Phase II Trial in Healthy Volunteers.

BACKGROUND: This study was designed to assess the efficacy of Bifidobacterium animalis ssp. lactis (Bl-04) for prevention of rhinovirus colds and to explore the interactions between the probiotic, the viral infection, the host response and the host microbiome. METHODS: The effect of ingestion of the probiotic Bl-04 was evaluated in a randomized, double-blinded rhinovirus (RV) challenge study. Healthy volunteers recruited from a university community in USA were randomized 1:1 using a computer generated code to ingest either Bl-04 (n=165) or placebo (n=169) for 28 days and were then challenged with RV-A39, and followed for 14 days. All study interactions and sample collection occurred in dedicated clinical research space. The primary analysis was the effect of the probiotic on the incidence of RV-associated illness. (Trial registration: NCT02679807, study complete). FINDINGS: The first cohort of volunteers was randomized on March 14, 2016 and the last (5th) cohort was randomized on March 12, 2018. Sixty-three (56%, 95% CI [47%; 66%]) of the 112 subjects in the active group and 60 (50%,95% CI [41%; 59%]) of the 120 subjects in the placebo group had a protocol-defined rhinovirus-associated illness (χ2=0·91, p=0·34). The point estimate of the difference in illness (active-placebo) is 6.3% (95% CI -6.7;19.1). There were no adverse events that were judged as definitely or probably related to the study product. INTERPRETATION: In this study there was no effect of orally administered Bl-04 on the occurrence of RV-associated illness. FUNDING: Danisco Sweeteners Oy (now IFF Health & Biosciences).

Identifying redox transition zones in the subsurface of a site with historical contamination.

Reactive iron mineral coatings found throughout reduction-oxidation (redox) transition zones play an important role in contaminant transformation processes. This research focuses on demonstrating a process for effectively delineating redox transition zones at a site with historical contamination. An 18.3 meter core was collected, subsampled, and preserved under anoxic conditions to maintain its original redox status. To ensure a high vertical resolution, sampling increments of 5.08 cm in length were analyzed for elemental concentrations with X-ray fluorescence (XRF), sediment pH, sediment oxidation-reduction potential (ORP), total volatile organic carbon (TVOC) concentration in the sample headspace, and abundant bacteria (16S rRNA sequencing). Over the core's length, gradients observed ranged from 3.74 to 8.03 for sediment pH, -141.4 mV to +651.0 mV for sediment ORP, and from below detection to a maximum of 9.6 ppm TVOC concentration (as chlorobenzene) in the headspace. The Fe and S gradients correlated with the presence of Fe and S reducing bacteria. S concentrations peaked in the Upper Zone and Zone 1 where Desulfosporosinus was abundant, suggesting precipitation of iron sulfide minerals. In Zone 2, Fe concentrations decreased where Geobacter was abundant, potentially resulting in Fe reduction, dissolution, and precipitation of minerals with increased solubility compared to the Fe(III) minerals. Using complementary geochemical and microbial data, five redox transition zones were delineated in the core collected. This research demonstrates a systematic approach to characterizing redox transition zones in a contaminated environment.

The Gut Microbiome and Xenobiotics: Identifying Knowledge Gaps.

There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut Microbiome: Markers of Human Health, Drug Efficacy and Xenobiotic Toxicity" (https://hesiglobal.org/event/the-gut-microbiome-workshop) to identify data gaps in determining how gut microbiome alterations may affect human health. Speakers and stakeholders from academia, government, and industry addressed multiple topics including the current science on the gut microbiome, endogenous and exogenous metabolites, biomarkers, and model systems. The workshop presentations and breakout group discussions formed the basis for identifying data gaps and research needs. Two critical issues that emerged were defining the microbial composition and function related to health and developing standards for models, methods and analysis in order to increase the ability to compare and replicate studies. A series of key recommendations were formulated to focus efforts to further understand host-microbiome interactions and the consequences of exposure to xenobiotics as well as identifying biomarkers of microbiome-associated disease and toxicity.

An Integrated Multi-Omics Analysis Defines Key Pathway Alterations in a Diet-Induced Obesity Mouse Model.

Obesity is a multifactorial disease with many complications and related diseases and has become a global epidemic. To thoroughly understand the impact of obesity on whole organism homeostasis, it is helpful to utilize a systems biological approach combining gene expression and metabolomics across tissues and biofluids together with metagenomics of gut microbial diversity. Here, we present a multi-omics study on liver, muscle, adipose tissue, urine, plasma, and feces on mice fed a high-fat diet (HFD). Gene expression analyses showed alterations in genes related to lipid and energy metabolism and inflammation in liver and adipose tissue. The integration of metabolomics data across tissues and biofluids identified major differences in liver TCA cycle, where malate, succinate and oxaloacetate were found to be increased in HFD mice. This finding was supported by gene expression analysis of TCA-related enzymes in liver, where expression of malate dehydrogenase was found to be decreased. Investigations of the microbiome showed enrichment of Lachnospiraceae, Ruminococcaceae, Streptococcaceae and Lactobacillaceae in the HFD group. Our findings help elucidate how the whole organism metabolome and transcriptome are integrated and regulated during obesity.

Safety evaluation of AB-LIFE(®) (Lactobacillus plantarum CECT 7527, 7528 and 7529): Antibiotic resistance and 90-day repeated-dose study in rats.

AB-LIFE(®) is a probiotic product consisting of equal parts of three strains of Lactobacillus plantarum (CECT 7527, 7528, and 7529) blended with inert excipients. Whole genome sequencing was performed on each of the three strains. Antibiotic resistance was evaluated by genomic mining for resistance genes, and assessment for transferability. No risk of transfer potential was identified for any antibiotic resistance genes in the three strains. AB-LIFE(®) was evaluated for potential subchronic oral toxicity in rats, with dosages of 300 and 1000 mg/kg BW/day (equivalent to 5.55 × 10(10) and 1.85 × 10(11) CFU/kg BW/day). Survival of the three test strains through the gastrointestinal tract was supported by fecal analysis. No adverse effects were identified with respect to in-life parameters, clinical or anatomic pathology, translocation, or fecal chemical analyses. The no-observed-adverse-effect level (NOAEL) for AB-LIFE(®) in male and female rats was 1000 mg/kg BW/day (1.85 × 10(11) CFU of AB-LIFE(®)/kg BW/day), the highest dose level evaluated. These results, in conjunction with a previous acute toxicity study in rats, support the conclusion that AB-LIFE(®) is safe for human consumption.

Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome.

The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both aquatic toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.

Modification of the BAX Salmonella test kit to include a hot start functionality (modification of AOAC Official Method 2003.09).

In 2010, the BAX System PCR assay for Salmonella was modified to include a hot start functionality designed to keep the reaction enzyme inactive until PCR begins. To validate the assay's Official Methods of Analysis status to include this procedure modification, an evaluation was conducted on four food types that were simultaneously analyzed with the BAX System and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual or the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook reference method for detecting Salmonella. Identical performance between the BAX System method and the reference methods was observed. Additionally, lysates were analyzed using both the BAX System Classic and BAX System Q7 instruments with identical results using both platforms for all samples tested. Of the 100 samples analyzed, 34 samples were positive for both the BAX System and reference methods, and 66 samples were negative by both the BAX System and reference methods, demonstrating 100% correlation. No instrument platform variation was observed. Additional inclusivity and exclusivity testing using the modified test kit demonstrated the test kit to be 100% accurate in evaluation of test panels of 352 Salmonella strains and 46 non-Salmonella strains.

DuPont qualicon BAX system real-time PCR assay for Escherichia coli O157:H7.

Evaluations were conducted to test the performance of the BAX System Real-Time PCR assay, which was certified as Performance Tested Method 031002 for screening E. coli O157:H7 in ground beef, beef trim, spinach, and lettuce. Method comparison studies performed on samples with low-level inoculates showed that the BAX System demonstrates a sensitivity equivalent or superior to the FDA-BAM and the USDA-FSIS culture methods, but with a significantly shorter time to result. Tests to evaluate inclusivity and exclusivity returned no false-negative and no false-positive results on a diverse panel of isolates, and tests for lot-to-lot variability and tablet stability demonstrated consistent performance. Ruggedness studies determined that none of the factors examined affect the performance of the assay. An accelerated shelf life study determined an initial 36 month shelf life for the test kit.

Evaluation of DuPont Qualicon Bax System PCR assay for yeast and mold.

Evaluations were conducted to test the performance of the BAX System PCR assay which was certified as Performance Tested Method 010902 for screening yeast and mold in yogurt, corn starch, and milk-based powdered infant formula. Method comparison studies performed on samples with low-level inoculates showed that the BAX System demonstrates a sensitivity equivalent to the U.S. Food and Drug Administration's Bacteriological Analytical Manual culture method, but with a significantly shorter time to obtain results. Tests to evaluate inclusivity and exclusivity returned no false-negative and no false-positive results on a diverse panel of isolates, and tests for lot-to-lot variability and tablet stability demonstrated consistent performance. Ruggedness studies determined that none of the factors examined affected the performance of the assay.

Drug-induced reversible lymphoid dyscrasia: a clonal lymphomatoid dermatitis of memory and activated T cells.

Certain systemic conditions predispose patients to excessive lymphocyte responses to immune-perturbing drugs, which may progress to malignant lymphoma. Many pathologists and clinicians believe that differentiation of pseudolymphoma from cutaneous T cell lymphoma (CTCL) can be reliably made through phenotypic and molecular analysis. We encountered 15 cases of atypical cutaneous T-cell lymphoid hyperplasia in the setting of drug therapy. We explored phenotypic anomalies using antibodies to CD2, 3, 4, 7, 8, 20, 30 and CD62 K and sought T-cell receptor gene rearrangements by a polymerase chain reaction methodology. The lymphoid infiltrates showed reproducible CD7 and/or CD62 K deletion in concert with T cell clonality and variable CD30 positivity-findings similar to those of CTCL-but the rashes resolved or improved substantially after drug modulation. We hypothesize that the infiltrates represent an unrepressed expansion of CD7- and CD62 K-negative activated memory T lymphocytes in response to antigenic triggers. We propose the term "drug-induced reversible lymphoid dyscrasia" to describe this entity.

Pityriasis lichenoides: a clonal T-cell lymphoproliferative disorder.

Pityriasis lichenoides (PL) is a papulosquamous disorder often considered a form of reactive dermatosis and classified with small plaque parapsoriasis (digitate dermatosis). However, some patients with PL have developed large plaque parapsoriasis (LPP) and mycosis fungoides (MF), and lymphoid atypia and T-cell clonality have been reported in lesions of PL. We set out to explore the possibility that PL is a form of T-cell dyscrasia. Cases were selected by natural language search from an outpatient dermatopathology database; 35 cases were reviewed and clinicians and patients were contacted. Hematoxylin and eosin-stained sections were examined and immunophenotyping was carried out on paraffin-embedded, formalin-fixed tissue using antibodies to CD2, CD3, CD4, CD5, CD7, CD8, CD20, CD30, and CD56. In paraffin-embedded tissue, T-cell receptor (TCR)-gamma chain rearrangement was sought through polymerase chain reaction single stranded conformational polymorphism analysis. There were 14 males and 21 females with a mean age of 40 years held clinically to have PL chronica (PLC) (28 cases) and/or PL et varioliformis acuta (PLEVA) (7 cases). Five patients developed large atrophic poikilodermatous and/or annular plaques compatible with MF and/or LPP in a background of typical PLC. All biopsies showed tropism of lymphocytes to an epidermis manifesting psoriasiform hyperplasia, dyskeratosis, parakeratosis, and intraepithelial collections of Langerhans' cells and lymphocytes mimicking Pautrier's microabascesses. Epidermal atrophy, dermal fibroplasia, poikilodermatous alterations, and a dominance of intraepidermal cerebriform cells were seen only in patients with chronic persistent disease (i.e., PLC) and in some cases corresponded with clinical progression to MF. All cases had a T cell-dominant infiltrate, with a CD7 deletion in 21 of 32 biopsies examined; the CD7-negative cells were typically the largest and most atypical forms, often in a cohesive array within the upper layers of the epidermis. In 17 biopsies in which a CD4 stain was satisfactory for evaluation, 50% or more of the intraepidermal population was CD4 positive in 8 biopsies, whereas in 11 biopsies 50% or more of the dermal infiltrate was CD4 positive. The CD4-positive cells frequently had a cerebriform nuclear morphology and were CD7 negative. Most cases had an admixture of CD8-positive lymphocytes in excess of 40% or more of the intraepidermal and/or dermal infiltrate; it was the dominant intraepidermal infiltrate in 10 cases. The CD8-positive cells, typically small, round, and CD7 positive, showed a directed pattern of migration into acrosyringia and suprapapillary plates, with satellitosis around CD4-positive/CD8-negative/CD7-negative atypical lymphocytes. CD56 positivity was seen among the intraepidermal lymphoid cells and roughly paralleled the CD8 profile. In general, CD8-positive lymphocytes dominated in cases of PLEVA, whereas CD4-positive lymphocytes were very conspicuous and composed the dominant intraepidermal populace only in those biopsies of progressive PL/PLC. Clonality was shown in 25 of 27 biopsies in which amplifiable DNA was obtained. Intraepithelial atypical lymphocytes, phenotypic abnormalities, and TCR-gamma rearrangements suggest that PLC and PLEVA are a form of T-cell dyscrasia. Lesions may follow a recalcitrant course characteristic of MF and premycotic disorders such as LPP. The aberrant phenotype cell is similar to that defining MF: a CD4-positive T lymphocyte with a CD5 and CD7 deletion. Directed epidermal migration seen in biopsies procured from incipient lesions along with occasional temporal association to viral or drug exposure suggests that an abnormal immune response to an antigenic trigger may be the inciting event.