The impact of botanical fermented foods on metabolic syndrome and type 2 diabetes: a systematic review of randomised controlled trials

Our systematic review assessed the impact of botanical fermented food (BFF) consumption on glucose, lipid, anthropometric, inflammatory and gut microbiota parameters, in adults with metabolic syndrome (MetS), MetS components or type 2 diabetes mellitus (T2DM). Embase, MEDLINE, Cochrane CENTRAL and Google Scholar were searched with no language limits, from inception to 31 August 2022, for eligible randomised controlled trials (RCTs). Two independent reviewers screened 6873 abstracts and extracted relevant data. Risk of bias (ROB) was assessed using the Cochrane Collaboration's ROB2 tool. The final review included twenty-six RCTs, with thirty-one reports published between 2001 and 2022. Significant (p < 0·05) within-group and between-group changes in cardiometabolic outcome means were reported in twenty-three and nineteen studies, respectively. Gut microbiota composition was assessed in four studies, with two finding significant between-group differences. No significant difference between groups of any measured outcomes was observed in five studies. There were fourteen studies at low ROB; ten were of some concern; and two were at high ROB. In 73% of included studies, BFF consumption by participants with obesity, MetS or T2DM led to significant between-group improvements in discrete cardiometabolic outcomes, including fasting blood glucose, lipid profile, blood pressure, waist circumference, body fat percentage and C-reactive protein. BFF consumption increased the abundance of beneficial gut bacteria, such as Bifidobacterium and LAB, whilst reducing potential pathogens such as Bacteroides. To determine the clinical significance of BFFs as therapeutic dietary adjuncts, their safety, tolerability and affordability must be balanced with the limited power and magnitude of these preliminary findings.

Diversity and succession of contaminating yeasts in white-brined cheese during cold storage

Contamination of white-brined cheeses (WBCs) with yeasts is of major concern in the dairy industry. This study aimed to identify yeast contaminants and characterize their succession in white-brined cheese during a shelf-life of 52 weeks. White-brined cheeses added herbs (WBC1) or sundried tomatoes (WBC2) were produced at a Danish dairy and incubated at 5 °C and 10 °C. An increase in yeast counts was observed for both products within the first 12-14 weeks of incubation and stabilized afterwards varying in a range of 4.19-7.08 log CFU/g. Interestingly, higher incubation temperature, especially in WBC2, led to lower yeast counts, concurrently with higher diversity of yeast species. Observed decrease in yeast counts was, most likely, due to negative interactions between yeast species leading to growth inhibition. In total, 469 yeast isolates from WBC1 and WBC2 were genotypically classified using the (GTG)₅-rep-PCR technique. Out of them, 132 representative isolates were further identified by sequencing the D1/D2 domain of the 26 S rRNA gene. Predominant yeast species in WBCs were Candida zeylanoides and Debaryomyces hansenii, while Candida parapsilosis, Kazachstania bulderi, Kluyveromyces lactis, Pichia fermentans, Pichia kudriavzevii, Rhodotorula mucilaginosa, Torulaspora delbrueckii, and Wickerhamomyces anomalus were found in lower frequency. Heterogeneity of yeast species in WBC2 was generally larger compared to WBC1. This study indicated that, along with contamination levels, taxonomic heterogeneity of yeasts is an important factor influencing yeast cell counts, as well as product quality during storage.

Age-related effects on the modulation of gut microbiota by pectins and their derivatives: an in vitro study

Introduction

The present study investigates whether supplementation with pectin-type polysaccharides has potential to improve aging-associated dysbiosis of the gut microbiota. The influence of different types of pectins on the gut microbiota composition and short-chain fatty acids (SCFAs) profiles of elderly was compared to younger adults.

Methods

Pectins studied included a pectin polysaccharide (PEC), a partially hydrolyzed pectin (PPH), and a pectin oligosaccharide (POS). Additionally, inulin was used as a reference prebiotic substrate. Individual fecal samples were collected from healthy elderly volunteers (70-75 years) and younger adults (30-35 years). In vitro fermentations were performed using the CoMiniGut model with controlled temperature and pH. Samples were withdrawn at baseline and after 24 h fermentation for measurement of SCFAs production and microbiota composition by 16S rRNA gene sequencing.

Results and Discussion

The results showed that fermentations with PEC and PPH resulted in a specific stimulation of Faecalibacterium prausnitzii regardless of the age groups. Collinsella aerofaciens became a dominating species in the young adult group with fermentations of all three pectins, which was not observed in the elderly group. No significant differences in SCFAs production were found among the pectins, indicating a high level of functional redundancy. Pectins boosted various bacterial groups differently from the reference prebiotic substrate (inulin). We also found inulin had reduced butyrogenic and bifidogenic effects in the elderly group compared to the younger adult group. In conclusion, the in vitro modulating effects of pectins on elderly gut microbiota showed potential of using pectins to improve age-related dysbiosis.

Iodine uptake of adrenal glands: A novel and reliable spectral dual-layer computed tomographic-derived biomarker for acute septic shock

OBJECTIVES

Septic shock is a potentially fatal condition. This study aims to assess whether iodine uptake and iodine density of abdominal organs on dual-layer spectral detector computed tomography (SDCT) could serve as a new imaging biomarker for patients in septic shock.

METHODS

Here, 95 patients who received contrast-enhanced abdominal CT examinations were included and separated into two groups: group A - septic shock; group B - no shock condition. Preselected abdominal (right and left adrenal gland, right and left kidney, infrarenal inferior vena cava (IVC), pancreas, spleen, and liver) localizations were independently evaluated by two radiologists, who measured iodine concentrations (mg/ml) and Hounsfield units (HU).

RESULTS

In all, 1520 measurements of iodine concentrations in mg/ml and HU were performed, with 27 patients in group A and 68 in group B. Iodine concentrations in mg/ml and HU correlated significantly in all organs measured. The corresponding correlation coefficient (r) ranged from 0.809 (pancreas) to 0.963 (right kidney). Inter-rater reliability (IRR) was very good for mg/ml (κ = 0.8; p < 0.01) and good for HU (κ = 0.773; p < 0.01) measurements. The mean iodine concentration and HU of the adrenal glands in septic and nonseptic patients was 4.88 ± 1.16 mg/ml/153 ± 36 HU and 2.67 ± 1.07 mg/ml/112 ± 41 HU, respectively. Iodine concentrations in the adrenal glands were significantly higher in group A than in group B patients (p < 0.01). The other organs remained unaffected and no significant difference was observed between patients in group A and B. Patients in group A presented significantly more often with an iodine uptake of >3.5 mg/ml of one adrenal gland (sensitivity = 0.926, specificity = 0.849, AUC = 0.951) or/and a combined concentration of >7 mg/ml of both adrenal glands (sensitivity = 0.889, specificity = 0.836, AUC = 0.928).

CONCLUSION

SDCT-derived iodine concentration of the adrenal glands could serve as a novel imaging biomarker for patients in acute septic shock. Our data suggest that an iodine uptake of >3.5 mg/ml of at least one adrenal gland or a combined iodine uptake of >7 mg/ml in both adrenal glands identifies patients in this condition.

The Potential of Pectins to Modulate the Human Gut Microbiota Evaluated by In Vitro Fermentation: A Systematic Review

Pectin is a dietary fiber, and its health effects have been described extensively. Although there are limited clinical studies, there is a growing body of evidence from in vitro studies investigating the effect of pectin on human gut microbiota. This comprehensive review summarizes the findings of gut microbiota modulation in vitro as assessed by 16S rRNA gene-based technologies and elucidates the potential structure-activity relationships. Generally, pectic substrates are slowly but completely fermented, with a greater production of acetate compared with other fibers. Their fermentation, either directly or by cross-feeding interactions, results in the increased abundances of gut bacterial communities such as the family of Ruminococcaceae, the Bacteroides and Lachnospira genera, and species such as Lachnospira eligens and Faecalibacterium prausnitzii, where the specific stimulation of Lachnospira and L. eligens is unique to pectic substrates. Furthermore, the degree of methyl esterification, the homogalacturonan-to-rhamnogalacturonan ratio, and the molecular weight are the most influential structural factors on the gut microbiota. The latter particularly influences the growth of Bifidobacterium spp. The prebiotic potential of pectin targeting specific gut bacteria beneficial for human health and well-being still needs to be confirmed in humans, including the relationship between its structural features and activity.

Central vein sign in patients with inflammatory lesion of the upper cervical spinal cord on susceptibility weighted imaging at 3 tesla. Preliminary results

BACKGROUND

A central vein sign (CVS) has been described in vivo in patients with MS but also in other inflammatory lesion of the brain such as neuromyelits optica spectrum disease and others. Recently, it has been used to differentiate patients with MS from other inflammatory lesions of the brain.

OBJECTIVE

It was the goal of this study to demonstrate the feasibility of the depiction of the CVS in patients with inflammatory lesion of the upper cervical spinal cord using susceptibility weighted imaging (SWI).

METHODS

Consecutive patients with inflammatory lesions of the upper cervical spinal cord were included. Patients were scanned using a 3 T Philips Ingenia CX. The presence of the CVS was assessed by two raters. Demographic and clinical parameters were compared between patients with and those without a CVS.

RESULTS

20 patients could be included. 15 patients had a diagnosis of MS. A CVS was present in 8 patients (40%). Agreement between the two raters was substantial (κ = 0.79). Time from first manifestation was significantly different (14 vs. 2 years, p = 0.021) between patients with CVS and without CVS.

CONCLUSION

The depiction of the CVS in the upper cervical spine is feasible. More research is necessary to evaluate these preliminary results and the value of the CVS in the spinal cord.

Analytical and Clinical Performance Evaluation of ARK Fentanyl II Assay on Beckman Coulter AU System

Introduction/Objective

Drugs of abuse, specifically opioids, have been in recent years an important focus in both medicine and media due to the ‘opioid epidemic’ and large numbers of overdose deaths. Synthetic opioids such as fentanyl have contributed to this epidemic. The CDC reports that of roughly 50,000 opioid overdose deaths in 2019, nearly 73% were due to synthetic opioids. The objective of this study is to assess the analytical and clinical performance of the Fentanyl II Assay by ARK Diagnostics, Inc.

Methods/Case Report

Fentanyl was qualitatively determined by the ARK Fentanyl II Assay, a homogenous enzyme immunoassay based on competition between drug in the specimen and drug labeled with recombinant glucose-6- phosphate dehydrogenase (rG6PDH) for antibody binding sites. The presence of drug in urine increases enzyme activity, which converts nicotinamide adenine dinucleotide (NAD) to NADH in the presence of glucose-6-phosphate, resulting in an absorbance change measured by spectrophotometry. The evaluation was performed following CLSI guidelines. The analytical performance was evaluated for accuracy and precision.

Results (if a Case Study enter NA)

To evaluate the accuracy, twelve positive and eight negative specimens were tested by the ARK immunoassay performed on two Beckman Coulter instruments (AU480 and AU680) and by LC- MS/MS. The results from both instruments showed 100% agreement with the results from LC-MS/MS. On instrument AU480, the within-run CVs were 18.0% at the level of 22.510 ng/mL and 0.8% at the level of 552.628 ng/mL. The between-run CVs were 8.8% at the level of 68.928 ng/mL and 3.7% at the level of 158.947 ng/mL. On instrument AU680, the within-run CVs were 273.4% at the level of 1.052 ng/mL and 0.8% at the level of 523.788 ng/mL. The between-run CVs were 7.8% at the level of 53.779 ng/mL and 3.1% at the level of 145.263 ng/mL. In May 2021, 2,075 fentanyl assays were run at UAB. Of those, 476 returned a positive result with a positive rate of 22.9%, and 1,599 were negative with a negative rate of 77.1%. One positive result was confirmed by LC-MS/MS as negative for fentanyl but positive for norfentanyl, a metabolite of fentanyl. The clinical specificity was 99.9% and sensitivity was 100%.

Conclusion

In Conclusion, the ARK fentanyl Assay II on Beckman Coulter AU system has good accuracy, sensitivity and specificity. The precision at medium and high levels are good. However, the precision at low level needs to be improved.

Occurrence of Yeasts in White-Brined Cheeses: Methodologies for Identification, Spoilage Potential and Good Manufacturing Practices

Yeasts are generally recognized as contaminants in the production of white-brined cheeses, such as Feta and Feta-type cheeses. The most predominant yeasts species are Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Kluyveromyces lactis, Rhodotorula mucilaginosa, and Trichosporon spp. Although their spoilage potential varies at both species and strain levels, yeasts will, in case of excessive growth, present a microbiological hazard, effecting cheese quality. To evaluate the hazard and trace routes of contamination, the exact taxonomic classification of yeasts is required. Today, identification of dairy yeasts is mainly based on DNA sequencing, various genotyping techniques, and, to some extent, advanced phenotypic identification technologies. Even though these technologies are state of the art at the scientific level, they are only hardly implemented at the industrial level. Quality defects, caused by yeasts in white-brined cheese, are mainly linked to enzymatic activities and metabolism of fermentable carbohydrates, leading to production of metabolites (CO2, fatty acids, volatile compounds, amino acids, sulfur compounds, etc.) and resulting in off-flavors, texture softening, discoloration, and swelling of cheese packages. The proliferation of spoilage yeast depends on maturation and storage conditions at each specific dairy, product characteristics, nutrients availability, and interactions with the co-existing microorganisms. To prevent and control yeast contamination, different strategies based on the principles of HACCP and Good Manufacturing Practice (GMP) have been introduced in white-brined cheese production. These strategies include milk pasteurization, refrigeration, hygienic sanitation, air filtration, as well as aseptic and modified atmosphere packaging. Though a lot of research has been dedicated to yeasts in dairy products, the role of yeast contaminants, specifically in white-brined cheeses, is still insufficiently understood. This review aims to summarize the current knowledge on the identification of contaminant yeasts in white-brined cheeses, their occurrence and spoilage potential related to different varieties of white-brined cheeses, their interactions with other microorganisms, as well as guidelines used by dairies to prevent cheese contamination.

Exploring the patient perspectives of mobile X-ray in nursing homes - A qualitative explorative pilot study

INTRODUCTION

For patients with dementia, behaviour and reactions to stimuli can change and an X-ray examination in the hospital can have be a frightening experience. The aim of this study was to identify the experiences and perspectives of patients with dementia and their caregivers on receiving a mobile x-ray examination in nursing homes.

METHODS

This study was designed as a qualitative study using patient observation and semi structured interviews, with a phenomenology-hermeneutic approach. In total, 23 patients were observed during X-ray examinations in nursing homes, and six semi structured interviews were conducted with the caregivers who participated in the examination.

RESULTS

The observations and interviews indicated that a known environment, a recognizable framework and calmness were central for a patient with dementia. The patients appeared calm and relaxed during the examination in their usual environment (nursing homes) where there are less stimuli and impressions based of the observations.

CONCLUSION

Mobile X-ray examinations for patients with dementia living in nursing homes had a positive impact on patients' reactions towards the X-ray examination. The examinations were performed in the patients' usual and safe environments, where impressions and stimuli were less disturbing for patients with dementia.

IMPLICATIONS FOR PRACTICE

The mobile x-ray unit can be of benefit for patients suffering from dementia and result in less impact. The patients living in nursing homes have the opportunity to be examined in their familiar environment, because of the mobile x-ray unit.

Probiotic potential of Saccharomyces cerevisiae and Kluyveromyces marxianus isolated from West African spontaneously fermented cereal and milk products

The yeast species Saccharomyces cerevisiae and Kluyveromyces marxianus are associated with fermentation of West African indigenous foods. The aim of this study was to characterize potential probiotic properties of S. cerevisiae and K. marxianus isolates from the West African milk products lait caillé and nunu and a cereal-based product mawè. The strains (14 in total) were identified by 26S rRNA gene sequencing and characterized for survival at gastrointestinal stress (bile salts and low pH) and adhesion to Caco-2 intestinal epithelial cells. Selected yeast isolates were tested for their effect on the transepithelial electrical resistance (TEER), using the intestinal epithelial cell line Caco-2 and for maintenance of intracellular pH (pH_i ) during perfusion with gastrointestinal pH (3.5 and 6.5). All tested yeasts were able to grow in bile salts in a strain-dependent manner, exhibiting a maximum specific growth rate (μ_max ) of 0.58-1.50 h^-1 . At pH 2.5, slow growth was observed for the isolates from mawè (μ_max of 0.06-0.80 h^-1 ), whereas growth of yeasts from other sources was mostly inhibited. Yeast adhesion to Caco-2 cells was strain specific and varied between 8.0% and 36.2%. Selected strains of S. cerevisiae and K. marxianus were able to maintain the pH_i homeostasis at gastrointestinal pH and to increase TEER across the Caco-2 monolayers, indicating their potential to improve intestinal barrier functions. Based on overall results, strains of K. marxianus and S. cerevisiae from mawè exhibited the highest probiotic potential and might be recommended for further development as starter cultures in West African fermented products.

The quorum-sensing molecule 2-phenylethanol impaired conidial germination, hyphal membrane integrity and growth of Penicillium expansum and Penicillium nordicum

AIMS

The aim of the study was to investigate the antifungal effects of a quorum sensing-molecule, 2-phenylethanol, against the food spoilage moulds Penicillium expansum and Penicillium nordicum.

METHODS AND RESULTS

Conidial germination of the tested Penicillium spp. (three strains in total) were inhibited by treatments with 2-phenylethanol in a concentration-dependent manner. Germinated conidia was significantly reduced from 4·4-16·7% at 7·5 mmol l^-1 and completely inhibited at 15 mmol l^-1 2-phenylethanol. Integrity of conidial cell membranes was unaffected by 2-phenylethanol resulting in reversible inhibition pattern of germination. In contrast, membrane permeability of actively growing hyphae was severely compromised, showing 63·5 - 75·7% membrane damage upon treatment with 15 mmol l^-1 2-phenylethanol. The overall inhibitory effect of 2-phenylethanol on colony development and growth of P. expansum and P. nordicum was additionally confirmed.

CONCLUSIONS

2-phenylethanol inhibits conidial germination and growth of P. expansum and P. nordicum in a nonlethal, reversible and concentration-dependent manner.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study indicates that 2-phenylethanol can find potential application as an antifungal agent for biological control of moulds in the food industry.

Data set for influence of blends of diesel and renewable fuels on compression ignition engine emissions

The present data article is based on the research work which investigates the influence of blends of diesel and renewable fuels on compression ignition engine emissions. In this experimental work, a 2.4 L, turbocharged, direct injection compression ignition engine and water brake dynamometer were used. Different ternary blends were created by mixing diesel, biodiesel and ethanol together in accordance with a mixture design of experiments. The homogeneity of each ternary blend was qualitatively checked by observing the samples for 24 hours for visible separation.

The engine was run over the WLTP drive cycle for each individual ternary blend and the exhaust emissions were recorded. NOVA 7466K and TESTO 350 gas analysers were used to record the exhaust emissions. A factory standard MAF sensor was used to record the inlet air mass flow and an aftermarket ECU was used to determine the fuel flow. The ternary blends were blended using standard laboratory measuring equipment.

Non-Contrast-Enhanced Carotid MRA: Clinical Evaluation of a Novel Ungated Radial Quiescent-Interval Slice-Selective MRA at 1.5T

BACKGROUND AND PURPOSE

Non-contrast-enhanced MRA techniques have experienced a renaissance due to the known correlation between the use of gadolinium-based contrast agents and the development of nephrogenic systemic fibrosis and the deposition of gadolinium in some brain regions. The purpose of this study was to assess the diagnostic performance of ungated non-contrast-enhanced radial quiescent-interval slice-selective MRA of the extracranial supra-aortic arteries in comparison with conventional contrast-enhanced MRA in patients with clinical suspicion of carotid stenosis.

MATERIALS AND METHODS

In this prospective study, both MRA pulse sequences were performed in 31 consecutive patients (median age, 68.8 years; 19 men). For the evaluation, the cervical arterial system was divided into 35 segments (right and left side). Three blinded reviewers separately evaluated these segments. An ordinal scoring system was used to assess the image quality of arterial segments and the stenosis grading of carotid arteries.

RESULTS

Overall venous contamination in quiescent-interval slice-selective MRA was rated as "none" by all readers in 84.9% of cases and in 8.1% of cases in contrast-enhanced MRA (P < .0001). The visualization quality of arterial segments was considered good to excellent in 40.2% for the quiescent-interval slice-selective MRA and in 52.2% for the contrast-enhanced MRA (P < .0001). The diagnostic accuracy of ungated quiescent-interval slice-selective MRA concerning the stenosis grading showed a total sensitivity and specificity of 85.7% and 90.0%, respectively.

CONCLUSIONS

Ungated quiescent-interval slice-selective MRA can be used clinically as an alternative to contrast-enhanced MRA without a significantly different image quality or diagnostic accuracy for the detection of carotid stenosis at 1.5T.

Impact of botanical fermented foods on metabolic biomarkers and gut microbiota in adults with metabolic syndrome and type 2 diabetes: a systematic review protocol

INTRODUCTION

Dysfunctional gut microbiota is a common finding in patients with metabolic syndrome (MetS) and type 2 diabetes mellitus (T2DM). Recent clinical trials have assessed whether botanical fermented foods (BFFs) have beneficial effects on metabolic biomarkers, inflammatory markers and gut microbiota. The aim of this review is to critically evaluate all randomised controlled trials (RCTs) of BFF for evidence of impact on the outcome measures of these disease states.

METHODS AND ANALYSIS

Four electronic databases (Embase, MEDLINE, CENTRAL and Google Scholar) as well as the grey literature will be searched from inception to present without language or publication status restrictions applied. Eligible RCTs which have enrolled adult participants with T2DM, any MetS components or combinations of these components, treated prophylactically or therapeutically with any botanical fermented food intervention, compared with a control group (no intervention, placebo or active control) will be assessed. Primary outcomes are related to the target conditions, including metabolic biomarkers, inflammatory markers and gut microbiota composition/function. Using Covidence, two independent investigators will conduct title and abstract screening, followed by full-text screening to identify appropriate studies. Methodological quality of the trials will be assessed using the Cochrane risk of bias assessment tool. Findings will be summarised with a narrative synthesis of the differences between included studies. A meta-analysis will be conducted if sufficient data are obtained.

ETHICS AND DISSEMINATION

Ethical approval is not required as primary data will not be collected. Results will be disseminated through peer-reviewed publication, conference presentations and press.

PROSPERO REGISTRATION NUMBER

CRD42018117766.

Potential of Pectins to Beneficially Modulate the Gut Microbiota Depends on Their Structural Properties

Pectins are plant cell-wall polysaccharides which can be utilized by commensal bacteria in the gut, exhibiting beneficial properties for the host. Knowledge of the impact of pectins on intestinal bacterial communities is insufficient and limited to a few types of pectins. This study characterized the relationship between the structural properties of pectins and their potential to modulate composition and activity of the gut microbiota in a beneficial way. For this purpose we performed in vitro fermentations of nine structurally diverse pectins from citrus fruits and sugar beet, and a pectic derivative, rhamnogalacturonan I (RGI), using a TIM-2 colon model. The composition of microbiota during TIM-2 fermentations was assessed by 16S rRNA gene amplicon sequencing. Both general and pectin-specific changes were observed in relative abundances of numerous bacterial taxa in a time-dependent way. Bacterial populations associated with human health, such as Faecalibacterium prausnitzii, Coprococcus, Ruminococcus, Dorea, Blautia, Oscillospira, Sutterella, Bifidobacterium, Christensenellaceae, Prevotella copri, and Bacteroides spp. were either increased or decreased depending on the substrate, suggesting that these bacteria can be controlled using structurally different pectins. The main structural features linked to the pectin-mediated shifts in microbiota included degree of esterification, composition of neutral sugars, distribution of homogalacturonan and rhamnogalacturonan fractions, degree of branching, and the presence of amide groups. Cumulative production of the total short chain fatty acids and propionate was largest in fermentations of the high methoxyl pectins. Thus, this study indicates that microbial communities in the gut can be specifically modulated by pectins and identifies the features in pectin molecules linked to microbial alterations. This knowledge can be used to define preferred dietary pectins, targeting beneficial bacteria, and favoring more balanced microbiota communities in the gut.

Modulation of gut microbiota from obese individuals by in vitro fermentation of citrus pectin in combination with Bifidobacterium longum BB-46

This study aimed to evaluate the effects of three treatments, i.e., Bifidobacterium longum BB-46 (T1), B. longum BB-46 combined with the pectin (T2), and harsh extracted pectin from lemon (T3) on obesity-related microbiota using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). The effects of the treatments were assessed by the analysis of the intestinal microbial composition (using 16S rRNA gene amplicon sequencing) and the levels of short-chain fatty acids (SCFAs) and ammonium ions (NH₄⁺). Treatments T2 and T3 stimulated members of the Ruminococcaceae and Succinivibrionaceae families, which were positively correlated with an increase in butyric and acetic acids. Proteolytic bacteria were reduced by the two treatments, concurrently with a decrease in NH₄⁺. Treatment T1 stimulated the production of butyric acid in the simulated transverse and descending colon, reduction of NH₄⁺ as well as the growth of genera Lactobacillus, Megamonas, and members of Lachnospiracea. The results indicate that both B. longum BB-46 and pectin can modulate the obesity-related microbiota; however, when the pectin is combined with B. longum BB-46, the predominant effect of the pectin can be observed. This study showed that the citric pectin is able to stimulate butyrate-producing bacteria as well as genera related with anti-inflammatory effects. However, prospective clinical studies are necessary to evaluate the anti/pro-obesogenic and inflammatory effects of this pectin for future prevention of obesity.

Vessel Wall Enhancement in Unruptured Intracranial Aneurysms: An Indicator for Higher Risk of Rupture? High-Resolution MR Imaging and Correlated Histologic Findings

BACKGROUND AND PURPOSE

Recent studies have suggested that wall enhancement of unruptured intracranial aneurysms in high-resolution MR imaging might serve as an imaging biomarker for higher risk of rupture. Histologic studies have revealed a possible association among inflammatory processes, degeneration, and destabilization of the aneurysm wall preceding rupture. Understanding the histologic condition underlying aneurysm wall enhancement could be an important step toward assessing the value of this method for risk stratification. We present our observations of aneurysm wall enhancement in MR vessel wall imaging and underlying histologic changes.

MATERIALS AND METHODS

We reviewed records of patients with an unruptured middle cerebral artery aneurysm who underwent MR vessel wall imaging before aneurysm clipping. Contrast enhancement of the aneurysm wall was dichotomized into either none/faint or strong. Histologic analysis included myeloperoxidase stain for detection of inflammatory cell invasion and CD34 stain for assessment of neovascularization and vasa vasorum.

RESULTS

Thirteen aneurysms were included. Five aneurysms showed strong wall enhancement. Among these, myeloperoxidase staining revealed inflammatory cell infiltration in 4. Three showed neovascularization. In 2 aneurysms, vasa vasorum were present. Seven aneurysms did not show wall enhancement; 1 had only mild enhancement. None of these bore evidence of inflammatory cell invasion or neovascularization, and they all lacked vasa vasorum.

CONCLUSIONS

Wall enhancement in MR vessel wall imaging is associated with inflammatory cell invasion, neovascularization, and the presence of vasa vasorum. Enhancement does not occur when histologic signs of inflammation are absent. Our results support the hypothesis that MR vessel wall imaging could provide valuable information for risk stratification.

The effect of pectins on survival of probiotic Lactobacillus spp. in gastrointestinal juices is related to their structure and physical properties

Pectins are plant polysaccharides used in food industry as gelling and stabilizing agents. This study investigated the ability of pectins to improve survival of probiotic species Lactobacillus fermentum PCC, L. reuteri RC-14, L. rhamnosus LGG and L. paracasei F-19 in simulated gastric solution in relationship to their structural and physical properties. Electrostatic interactions between pectins and bacteria were evaluated by the Zeta-potential approach. Bacterial survival was assessed by flow cytometry and plate counting. L. fermentum PCC and L. reuteri RC-14 were more resistant to gastric conditions; their survival rate was further improved in the presence of five out of ten tested pectins. Additionally, two of the pectins had a positive effect on viability of the less resistant L. rhamnosus LGG and L. paracasei F-19. The beneficial effect was generally observed for the high-methoxylated pectins, indicating that substituted polygalacturonic acid in the backbone is essential for bacterial protection. Other pectin features associated with improved survival, included less negative Zeta-potential, higher molecular weight, as well as lower values of hydrodynamic sizes, viscosity and degree of branching. The study indicates that pectins have a potential to protect probiotic bacteria through the gastro-intestinal transit and identifies the features linked to their functionality.

Abstract P1-10-08: Development of a first-in-class oral selective ERα covalent antagonist (SERCA) for the treatment of ERαWT and ERαMUT breast cancer

Mutations in estrogen receptor alpha (ERα) are detected in up to 30% of breast cancer patients who have relapsed during endocrine therapy. ERα mutations functionally confer resistance to existing classes of endocrine therapies, likely through gaining constitutive activity. The fact that current ER-directed therapies are only partially effective in the ERα mutant setting, and that a significant proportion of resistant breast cancer metastases continue to remain dependent on ERα signaling for growth/survival, highlights the critical need to develop the next generation of ERα antagonists that can overcome aberrant ERα activity. Using structure-based drug design approaches we have identified a novel class of ERα antagonist referred to as Selective ERα Covalent Antagonist (SERCA) that inactivate both wild-type and mutant ERα by targeting a unique cysteine residue that is not conserved among other steroid hormone receptors. Biophysical, biochemical and cellular analyses confirm the covalent mechanism of action, specific binding to ER and selective inhibition of ERα-dependent transcription of SERCAs. H3B-6545 is a highly selective SERCA that potently antagonizes wild-type and mutant ERα in biochemical and cell based assays demonstrating increased potency over standard of care and other experimental agents. In vivo, H3B-6545 shows superior efficacy to fulvestrant in the MCF-7 xenograft model with once daily oral dosing, achieving maximal antitumor activity at doses &gt;10x below the maximum tolerated dose in mice. In addition, H3B-6545 shows superior antitumor activity to both tamoxifen and fulvestrant in patient derived xenograft models of breast cancer carrying estrogen receptor mutations. In summary, H3B-6545 is a first-in-class, orally available and selective ER covalent antagonist with a compelling pre-clinical profile that is being developed for the treatment of ERα positive breast cancer.

Citation Format: Korpal M, Puyang X, Furman C, Zheng GZ, Banka D, Wu J, Zhang Z, Thomas M, Mackenzie C, Yao H, Rimkunas V, Kumar P, Caleb B, Karr C, Subramanian V, Irwin S, Larsen N, Vaillancourt F, Nguyen T-V, Davis A, Chan B, Hao MH, O'Shea M, Prajapati S, Agoulnik S, Kuznetsov G, Kumar N, Yu Y, Lai G, Hart A, Eckley S, Fekkes P, Bowser T, Joshi JJ, Selvaraj A, Wardell S, Norris J, Smith S, Reynolds D, Mitchell L, Wang J, Yu L, Kim A, Rioux N, Sahmoud T, Warmuth M, Smith PG, Zhu P. Development of a first-in-class oral selective ERα covalent antagonist (SERCA) for the treatment of ERαWT and ERαMUT breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-10-08.

Moderate to severe hidradenitis suppurativa patients do not have an altered bacterial composition in peripheral blood compared to healthy controls

BACKGROUND

Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease defined by recurrent nodules, tunnels and scarring involving the intertriginous skin. Patients with HS often report an array of systemic symptoms such as fatigue and malaise. The aetiology of these symptoms remains unclear. Previously, various bacteria have been associated with mature HS lesions, and bacteraemia has been reported in patients with HS using traditional culturing methods. Thus, we hypothesized that a low-grade bacteraemia contributes to the symptomatology in patients with HS.

OBJECTIVE

To explore the potential presence of bacteraemia in patients with HS and healthy controls.

METHOD

A case-control study. Compositions of bacteria in the blood of 27 moderate to severe HS patients and 26 healthy controls were investigated using next-generation 16S ribosomal RNA gene sequencing (NGS) and routine anaerobic and aerobic blood culturing. None of the participants received any antibiotics (systemic or topical therapy) within 1 month prior to the study. HS patients with a recent flare were randomly selected by consecutive recruitment of eligible patients from the Department of Dermatology, Zealand University Hospital, Denmark. Healthy controls were recruited from the University of Copenhagen as well as from the healthcare staff.

RESULTS

The different bacterial compositions were investigated using NGS and traditional anaerobic and aerobic blood culturing. Our NGS analysis provided a previously unreported characterization of the bacterial composition in peripheral blood from patients with HS and healthy controls. Overall, our data demonstrated that patients with HS do not have a different bacterial composition in their peripheral blood than healthy controls.

CONCLUSION

The study suggests that the self-reported symptoms in HS such as malaise and fatigue may not be linked to bacteraemia.

Transcriptome analysis of Lactococcus lactis subsp. lactis during milk acidification as affected by dissolved oxygen and the redox potential

Performance of Lactococcus lactis as a starter culture in dairy fermentations depends on the levels of dissolved oxygen and the redox state of milk. In this study the microarray analysis was used to investigate the global gene expression of L. lactis subsp. lactis DSM20481(T) during milk acidification as affected by oxygen depletion and the decrease of redox potential. Fermentations were carried out at different initial levels of dissolved oxygen (dO2) obtained by milk sparging with oxygen (high dO2, 63%) or nitrogen (low dO2, 6%). Bacterial exposure to high initial oxygen resulted in overexpression of genes involved in detoxification of reactive oxygen species (ROS), oxidation-reduction processes, biosynthesis of trehalose and down-regulation of genes involved in purine nucleotide biosynthesis, indicating that several factors, among them trehalose and GTP, were implicated in bacterial adaptation to oxidative stress. Generally, transcriptional changes were more pronounced during fermentation of oxygen sparged milk. Genes up-regulated in response to oxygen depletion were implicated in biosynthesis and transport of pyrimidine nucleotides, branched chain amino acids and in arginine catabolic pathways; whereas genes involved in salvage of nucleotides and cysteine pathways were repressed. Expression pattern of genes involved in pyruvate metabolism indicated shifts towards mixed acid fermentation after oxygen depletion with production of specific end-products, depending on milk treatment. Differential expression of genes, involved in amino acid and pyruvate pathways, suggested that initial oxygen might influence the release of flavor compounds and, thereby, flavor development in dairy fermentations. The knowledge of molecular responses involved in adaptation of L. lactis to the shifts of redox state and pH during milk fermentations is important for the dairy industry to ensure better control of cheese production.

Characteristics and phylogeny of Bacillus cereus strains isolated from Maari, a traditional West African food condiment

Maari is a spontaneously fermented food condiment made from baobab tree seeds in West African countries. This type of product is considered to be safe, being consumed by millions of people on a daily basis. However, due to the spontaneous nature of the fermentation the human pathogen Bacillus cereus occasionally occurs in Maari. This study characterizes succession patterns and pathogenic potential of B. cereus isolated from the raw materials (ash, water from a drilled well (DW) and potash), seed mash throughout fermentation (0-96h), after steam cooking and sun drying (final product) from two production sites of Maari. Aerobic mesophilic bacterial (AMB) counts in raw materials were of 10(5)cfu/ml in DW, and ranged between 6.5×10(3) and 1.2×10(4)cfu/g in potash, 10(9)-10(10)cfu/g in seed mash during fermentation and 10(7) - 10(9) after sun drying. Fifty three out of total 290 AMB isolates were identified as B. cereus sensu lato by use of ITS-PCR and grouped into 3 groups using PCR fingerprinting based on Escherichia coli phage-M13 primer (M13-PCR). As determined by panC gene sequencing, the isolates of B. cereus belonged to PanC types III and IV with potential for high cytotoxicity. Phylogenetic analysis of concatenated sequences of glpF, gmk, ilvD, pta, pur, pycA and tpi revealed that the M13-PCR group 1 isolates were related to B. cereus biovar anthracis CI, while the M13-PCR group 2 isolates were identical to cereulide (emetic toxin) producing B. cereus strains. The M13-PCR group 1 isolates harboured poly-γ-D-glutamic acid capsule biosynthesis genes capA, capB and capC showing 99-100% identity with the environmental B. cereus isolate 03BB108. Presence of cesB of the cereulide synthetase gene cluster was confirmed by PCR in M13-PCR group 2 isolates. The B. cereus harbouring the cap genes were found in potash, DW, cooking water and at 8h fermentation. The "emetic" type B. cereus were present in DW, the seed mash at 48-72h of fermentation and in the final product, while the remaining isolates (PanC type IV) were detected in ash, at 48-72h fermentation and in the final product. This work sheds light on the succession and pathogenic potential of B. cereus species in traditional West African food condiment and clarifies their phylogenetic relatedness to B. cereus biovar anthracis. Future implementation of GMP and HACCP and development of starter cultures for controlled Maari fermentations will help to ensure a safe product.

Neonatal levels of neurotrophic factors and risk of autism spectrum disorders

OBJECTIVE

To examine levels of 3 neurotrophic factors (NTFs): Brain derived neurotrophic factor (BDNF), Neurotrophin-4 (NT-4), and transforming growth factor-β (TGF-β) in dried blood spot samples of neonates diagnosed with autism spectrum disorders (ASD) later in life and frequency-matched controls.

METHOD

Biologic samples were retrieved from the Danish Newborn Screening Biobank. NTFs for 414 ASD cases and 820 controls were measured using Luminex technology. Associations were analyzed with continuous measures (Tobit regression) as well as dichotomized at the lower and upper 10th percentiles cutoff points derived from the controls' distributions (logistic regression).

RESULTS

ASD cases were more likely to have BDNF levels falling in the lower 10th percentile (odds ratios [OR], 1.53 [95% confidence intervals (CI), 1.04-2.24], P-value = 0.03). Similar pattern was seen for TGF-β in females with ASD (OR, 2.36 [95% CI, 1.05-5.33], P-value = 0.04). For NT-4, however, ASD cases diagnosed with ICD-10 only were less likely to have levels in upper 10th percentile compared with controls (OR, 0.22 [95% CI, 0.05-0.98], P-value = 0.05).

CONCLUSION

Results cautiously indicate decreased NTFs levels during neonatal period in ASD. This may contribute to the pathophysiology of ASD through impairments of neuroplasticity. Further research is required to confirm our results and to examine the potential therapeutic effects of NTFs in ASD.

Effect of Lactobacillus salivarius Ls-33 on fecal microbiota in obese adolescents

BACKGROUND & AIMS

This study is a part of the clinical trials with probiotic bacterium Lactobacillus salivarius Ls-33 conducted in obese adolescents. Previously reported clinical studies showed no effect of Ls-33 consumption on the metabolic syndrome in the subject group. The aim of the study was to investigate the impact of L. salivarius Ls-33 on fecal microbiota in obese adolescents.

METHODS

The study was a double-blinded intervention with 50 subjects randomized to intake of L. salivarius Ls-33 or placebo for 12 weeks. The fecal microbiota was assessed by real-time quantitative PCR before and after intervention. Concentrations of fecal short chain fatty acids were determined using gas chromatography.

RESULTS

Ratios of Bacteroides-Prevotella-Porphyromonas group to Firmicutes belonging bacteria, including Clostridium cluster XIV, Blautia coccoides_Eubacteria rectale group and Roseburia intestinalis, were significantly increased (p ≤ 0.05) after administration of Ls-33. The cell numbers of fecal bacteria, including the groups above as well as Clostridium cluster I, Clostridium cluster IV, Faecalibacterium prausnitzii, Enterobacteriaceae, Enterococcus, the Lactobacillus group and Bifidobacterium were not significantly altered by intervention. Similarly, short chain fatty acids remained unaffected.

CONCLUSION

L. salivarius Ls-33 might modify the fecal microbiota in obese adolescents in a way not related to metabolic syndrome.

CLINICAL TRIAL NUMBER

NCT 01020617.

Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults

BACKGROUND

Recent evidence suggests that there is a link between metabolic diseases and bacterial populations in the gut. The aim of this study was to assess the differences between the composition of the intestinal microbiota in humans with type 2 diabetes and non-diabetic persons as control.

METHODS AND FINDINGS

The study included 36 male adults with a broad range of age and body-mass indices (BMIs), among which 18 subjects were diagnosed with diabetes type 2. The fecal bacterial composition was investigated by real-time quantitative PCR (qPCR) and in a subgroup of subjects (N = 20) by tag-encoded amplicon pyrosequencing of the V4 region of the 16S rRNA gene. The proportions of phylum Firmicutes and class Clostridia were significantly reduced in the diabetic group compared to the control group (P = 0.03). Furthermore, the ratios of Bacteroidetes to Firmicutes as well as the ratios of Bacteroides-Prevotella group to C. coccoides-E. rectale group correlated positively and significantly with plasma glucose concentration (P = 0.04) but not with BMIs. Similarly, class Betaproteobacteria was highly enriched in diabetic compared to non-diabetic persons (P = 0.02) and positively correlated with plasma glucose (P = 0.04).

CONCLUSIONS

The results of this study indicate that type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. The level of glucose tolerance should be considered when linking microbiota with metabolic diseases such as obesity and developing strategies to control metabolic diseases by modifying the gut microbiota.

Biomechanical and tissue handling property comparison of decellularized and cryopreserved tibialis anterior tendons following extreme incubation and rehydration

Little is known regarding the biomechanical profiles and tissue handling properties of decellularized and cryopreserved human tibialis anterior tendons prepared as allografts for ACL reconstruction. This study compared allografts prepared using two extremes of the same cryoprotectant incubation and rehydration technique with a standardly prepared control group. Porcine tibiae with similar apparent BMD were randomly divided into three groups of ten specimens. Paired tendons were randomly divided into two experimental groups: Group 1 = 8 h incubation/15 min rehydration; Group 2 = 2 h incubation/1 h rehydration. Group 3 (control) consisted of ten standardly prepared tendons with 20 min rehydration. Tissue handling properties were graded during allograft preparation using a modified visual analog scale. Similar diameter allografts were fixed in matched diameter extraction drilled tibial tunnels with 35 mm long, 1 mm > tunnel diameter bioabsorbable interference screws. Potted constructs were mounted in a servo hydraulic device, pretensioned between 10-50 N at 0.1 Hz (10 cycles), and isometric pretensioned at 50 N for 1 min, prior to 500 submaximal loading cycles (50-250 N) at 0.5 Hz, and load to failure testing (20 mm/min). Constructs prepared under extreme conditions generally displayed comparable biomechanical properties to the control condition. Group 1 (8 h incubation/15 min rehydration)(-34 +/- 35 ms) and Group 2 (2 h incubation/1 h rehydration) (-22 +/- 38 ms) displayed smaller mean displacement-load peak phase timing differences over the initial ten cycles compared to Group 3 (control)(-42 +/- 49 ms), P = 0.004, suggesting greater relative construct stiffness. Group 1 (8 h incubation/15 min rehydration) (234.9 +/- 34 N/mm) and Group 2 (2 h incubation/1 h rehydration)(231.3 +/- 43 N/mm) displayed lower construct stiffness during load to failure testing than Group 3 (control)(284.5 +/- 25.2 N/mm), P = 0.003. Group 1 (8 h incubation/15 min rehydration) differed from Group 2 (2 h incubation/1 h rehydration) and Group 3 (control) for perceived tensile stiffness (2.4 +/- 2.0 vs. 7.0 +/- 0.5 and 7.9 +/- 0.3, respectively), compressive resilience (1.7 +/- 0.8 vs. 5.9 +/- 1.0 and 7.8 +/- 0.4, respectively), handling ease (2.8 +/- 1.0 vs. 6.5 +/- 0.5 and 7.0 +/- 0.7, respectively), color (2.6 +/- 0.8 vs. 4.7 +/- 0.7 and 5.1 +/- 0.3, respectively) and texture (4.0 +/- 0.8 vs. 6.2 +/- 0.8 and 6.8 +/- 0.8, respectively) (P < 0.0001). Group 2 (2 h incubation/1 h rehydration)(6.0 +/- 0.7 and 5.9 +/- 1.0, respectively) also differed from Group 3 (control)(6.8 +/- 0.8 and 7.8 +/- 0.4, respectively) for general "feel" and compressive resilience (P < 0.0001). Tensile stiffness and compressive resilience displayed moderate and weak relationships, respectively with displacement during submaximal cyclic loading (r2 = 0.78 and 0.58, respectively), stiffness (r2 = 0.33 and 0.44, respectively) and load at failure (r2 = 0.59 and 0.37, respectively) for Group 3 (control), but not for experimental Group 1 (8 h incubation/15 min rehydration) or Group 2 (2 h incubation/1 h rehydration). Knee surgeons should be aware that soft tissue tendon decellularization and cryopreservation may change the biomechanical stiffness, tissue handling properties, and relationships between these variables compared to standardly prepared allograft tissue.

The effect of calcium ions on adhesion and competitive exclusion of Lactobacillus ssp. and E. coli O138

The adhesion abilities of 11 strains of Lactobacillus were determined in vitro using the IPEC-J2 cell line as a model system. Bacteria cultures included the probiotic strains L. rhamnosus GG, L. reuteri ATCC 55730, L. johnsonii NCC 533 and L. reuteri DSM 12246, and new isolates of Lactobacillus ssp. Adhesion was quantified by scintillation counting of radiolabelled bound bacteria. The highest adhesion of 38%, was determined for L. reuteri DSM 12246 followed by L. plantarum Q47 with an adhesion level of 24%. Other strains showed moderate to low binding of less than 16%. Competitive adhesion experiments on IPEC-J2 cells demonstrated that strongly adhesive strains, as L. reuteri DSM 12246 and L. plantarum Q47, significantly reduced the attachment of the less adhesive strains, such as L. rhamnosus GG and L. johnsonii NCC 533, both under condition of co-incubation and in displacement assays, indicating that bacteria may share the same binding sites for attachment to intestinal cells. Furthermore, it was revealed that calcium ions significantly increased the binding of tested lactobacilli to IPEC-J2 cells; and therefore, added calcium may be useful in enhancing the adhesion of normally weakly adhesive probiotic cultures. In contrast, no significant change in adhesion of lactobacilli was observed in the presence of Mg and Zn ions. Displacement assays performed with pathogenic E. coli O138 showed that all tested Lactobacillus strains reduced the attachment of E. coli O138 to IPEC-J2 by more than 2-fold both in the presence and the absence of calcium ions. The strains of Lactobacillus did not differ significantly in the extent of their inhibition of E. coli O138 adhesion, indicating that the reduced adhesion of E. coli O138 was due to steric hindrance of the binding sites rather than to specific interactions.

Dynamic role of kallikrein 6 in traumatic spinal cord injury

Kallikrein 6 (K6) is a member of the kallikrein gene family that comprises 15 structurally and functionally related serine proteases. In prior studies we showed that, while this trypsin-like enzyme is preferentially expressed in neurons and oligodendroglia of the adult central nervous system (CNS), it is up-regulated at sites of injury due to expression by infiltrating immune and resident CNS cells. Given this background we hypothesized that K6 is a key contributor to the pathophysiology of traumatic spinal cord injury (SCI), influencing neural repair and regeneration. Examination of K6 expression following contusion injury to the adult rat cord, and in cases of human traumatic SCI, indicated significant elevations at acute and chronic time points, not only at the injury site but also in cord segments above and below. Elevations in K6 were particularly prominent in macrophages, microglia and reactive astrocytes. To determine potential effects of elevated K6 on the regeneration environment, the ability of neurons to adhere to and extend processes on substrata which had been exposed to recombinant K6 was examined. Limited (1 h) or excess (24 h) K6-mediated proteolytic digestion of a growth-facilitatory substrate, laminin, significantly decreased neurite outgrowth. By contrast, similar hydrolysis of a growth-inhibitory substrate, aggrecan, significantly increased neurite extension and cell adherence. These data support the hypothesis that K6 enzymatic cascades mediate events secondary to spinal cord trauma, including dynamic modification of the capacity for axon outgrowth.

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at http://greengenes.lbl.gov/NAST. Each user-submitted sequence is compared with Greengenes' 'Core Set', comprising approximately 10,000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.