Profiling novel lateral gene transfer events in the human microbiome

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.

Personalised azithromycin+metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn's disease (CD): protocol of a pilot study

INTRODUCTION

Early relapse in Crohn's disease (CD) is associated with a more severe disease course. The microbiome plays a crucial role, yet strategies targeting the microbiome are underrepresented in current guidelines. We hypothesise that early manipulation of the microbiome will improve clinical response to standard-of-care (SOC) induction therapy in patients with a relapse-associated microbiome profile. We describe the protocol of a pilot study assessing feasibility of treatment allocation based on baseline faecal microbiome profiles.

METHODS AND ANALYSIS

This is a 52-week, multicentre, randomised, controlled, open-label, add-on pilot study to test the feasibility of a larger multicontinent trial evaluating the efficacy of adjuvant antibiotic therapy in 20 paediatric patients with mild-to-moderate-CD (10<PCDAI≤37.5; PCDAI, Pediatric Crohn's Disease Activity Index). SOC induction treatment will be Crohn's Disease Exclusion Diet+Partial Enteral Nutrition (CDED+PEN). Relapse-associated microbiome signatures will be evaluated using 16S rRNA gene sequencing and a previously generated Bayesian predictive model (BioMiCo) based on baseline stool. At week 4, patients in remission with relapse-associated signatures (group A) will be randomised to CDED+antibiotics (A2) or CDED+PEN alone (A1). Patients in remission without this signature will continue CDED+PEN alone (B). Patients not in remission will receive CDED+antibiotics regardless of their microbiome signature (C). Subjects in group A2 or C will receive a combination of azithromycin 7.5 mg/kg (weeks 4-8: 5 days/week; weeks 9-12: 3 days/week) with metronidazole 20 mg/kg/day (weeks 4-12). Primary outcomes will assess feasibility of treatment allocation and possible efficacy to sustain remission (PCDAI≤10, no need for reinduction). Exploratory outcomes will include changes in PCDAI, inflammatory markers and patient-reported outcomes. We will additionally explore changes in faecal microbiome taxonomic composition between groups.

ETHICS AND DISSEMINATION

This study was approved by METC-AMC and CCMO (Netherlands) and IWK Health Centre (Canada). The first version of this protocol was approved by North Carolina Children's Hospital (USA), Wolfson Medical Centre (Israel). The FDA (USA), Health Canada and Ministry of Health (Israel) have reviewed and approved the protocol. Results will be published in international peer-reviewed journals and summaries will be provided to the funders and participants.

TRIAL REGISTRATION NUMBER

NCT04186247.

Proteome and secretome profiling of zinc availability in Cryptococcus neoformans identifies Wos2 as a subtle influencer of fungal virulence determinants

BACKGROUND

Fungal infections impact over 25% of the global population. For the opportunistic fungal pathogen, Cryptococcus neoformans, infection leads to cryptococcosis. In the presence of the host, disease is enabled by elaboration of sophisticated virulence determinants, including polysaccharide capsule, melanin, thermotolerance, and extracellular enzymes. Conversely, the host protects itself from fungal invasion by regulating and sequestering transition metals (e.g., iron, zinc, copper) important for microbial growth and survival.

RESULTS

Here, we explore the intricate relationship between zinc availability and fungal virulence via mass spectrometry-based quantitative proteomics. We observe a core proteome along with a distinct zinc-regulated protein-level signature demonstrating a shift away from transport and ion binding under zinc-replete conditions towards transcription and metal acquisition under zinc-limited conditions. In addition, we revealed a novel connection among zinc availability, thermotolerance, as well as capsule and melanin production through the detection of a Wos2 ortholog in the secretome under replete conditions.

CONCLUSIONS

Overall, we provide new biological insight into cellular remodeling at the protein level of C. neoformans under regulated zinc conditions and uncover a novel connection between zinc homeostasis and fungal virulence determinants.

Enhancement of gut barrier function by microbial metabolite, urolithin A via AhR-Nrf2 dependent pathways in IBD

Inflammatory bowel diseases (IBD) consisting of Crohn’s and ulcerative colitis are resultant of dysregulation of the immune system leading to intestinal inflammation and microbial dysbiosis. Numerous studies in recent years highlighted the pivotal role of gut microbiota and their metabolites in host physiological processes including in IBD. Urolithin A (UroA) is a microbial metabolite derived from polyphenolics (e.g., ellagitannins/ellagic acid) of pomegranate and berries. We also synthesized a potent structural analogue of UroA (UAS03) and tested their efficacies in preventing and treating colitis in pre-clinical models. Our studies showed that UroA/UAS03 significantly enhance gut barrier function in addition to blocking unwarranted inflammation. We demonstrate that UroA and UAS03 exert their barrier functions through activation of aryl hydrocarbon receptor (AhR)- nuclear factor erythroid 2–related factor 2 (Nrf2)-dependent pathways to upregulate epithelial tight junction proteins. In addition, treatment with these compounds attenuated colitis in pre-clinical models by remedying barrier dysfunction and blocking increased inflammatory mediators such as IL-6, TNF-α and IL-1β. UroA/UAS03 failed to induce tight junction proteins and protect against 2,4,6-Trinitrobenzenesulfonic acid (TNBS)-induced colitis in AhR−/− and Nrf2−/− mice suggesting an obligatory requirement of AhR and Nrf2 pathways for UroA/UAS03 mediated beneficial activities. Overall, the results highlight how microbial metabolites provide two-pronged beneficial activities at gut epithelium by enhancing barrier functions and reducing systemic and local inflammation to protect from colonic diseases.

Selective sensitivity of the gut microbiome to iron chelators in polybacterial abdominal sepsis

Iron chelation has been proposed as a potential therapy for polybacterial abdominal sepsis. Treatment with iron chelation is known to be able to attenuate bacterial growth. It is hypothesized that the different types of bacteria will exhibit variations in their sensitivity to iron chelation based on differences in their iron metabolism. Bacteria with weaker iron access systems might have their growth reduced initially, but stronger species may also be suppressed. Gram-positive and Gram-negative bacteria are known to possess different iron acquisition systems, which may affect their response to iron chelation. Bacteria which can produce siderophores are at a particular advantage for iron acquisition. Novel iron chelators, which do not act as xenosiderophores, may be effective in depriving these bacteria of iron. This has implications for the treatment of polybacterial sepsis, which might be enhanced if the sensitivity to iron chelation of the primary causative agents is known.

Frontal sinus cells: identification, prevalence, and association with frontal sinus mucosal thickening

BACKGROUND

Frontal sinus cells (FSCs) are thought to be a potential cause of narrowing of frontal recess outflow. It remains unclear if FSCs are associated with frontal sinus mucosal thickening and chronic rhinosinusitis. The goal of the current study is to determine the prevalence of FSCs and their association with frontal sinus mucosal thickening.

METHODS

All adult patients undergoing computed tomography (CT) scans of the paranasal sinuses at our institution between February and October 2010 were reviewed. All CT scans were evaluated for the presence of FSC (types 1-4) and association with frontal mucosal thickening. The secondary outcome measure was to examine interrater agreement between two raters who independently evaluated all CT scans.

RESULTS

Analysis of 399 CT scans was performed with 71 scans excluded. The proportion of patients with FSC type 1 was 26%, 6.4% was type 2 cells, 2.1% was type 3 cells, and 0% was type 4 cells. The odds ratio of mucosal thickening for type 1 FSCs was 15.9 (95% CI, 9.8-25.7), type 2 was 13.7 (95% CI, 6.7-27.8), and type 3 was 9.5 (95% CI, 3.0-30.2). Interrater agreement for the evaluation of mucosal thickening was high (kappa, 0.69-0.76; p = 0.001). Agreement for the presence or absence of FSCs was moderate (kappa, 0.392; p = 0.001).

CONCLUSION

There is a significant association of frontal sinus mucosal thickening with the presence of FSCs. Independent raters have moderate agreement when identifying the presence and type of FSCs.

Total glossectomy with laryngeal preservation and free flap reconstruction: objective functional outcomes and systematic review of the literature

OBJECTIVE

Advanced tongue cancer is a devastating diagnosis with potential for significant morbidity after treatment. This is especially true for patients undergoing total glossectomy with laryngeal preservation (TGLP), free flap reconstruction and adjuvant radiotherapy. The goals of this study were to: 1) determine long-term objective functional and quality of life outcomes, 2) investigate the influence of rehabilitation on functional recovery and 3) determine swallowing ability in patients with TGLP.

STUDY DESIGN

Prospective cohort study and systematic review of the literature.

METHODS

Functional outcomes data were collected from 2000-2010. Outcomes were measured pre- and 12 months post-surgery and included: gastrostomy-tube (G-Tube) rates, swallowing transit times on video fluoroscopic swallowing studies, speech intelligibility and EORTC-H&N 35 quality of life scores. A systematic review of the literature was conducted to determine comprehensive long term G-Tube rates.

RESULTS

Twelve patients were included and eight were still living at 12 months post-surgery. Fifty percent of patients in this study and 24% with systematic review used G-Tubes at 1 year post-surgery. Patients who could swallow did not aspirate, but more than doubled swallowing transit times. Spoken sentence intelligibility averaged 66% and mean quality of life scores improved 8.9 points 12 months post-surgery. Patients who attended >80% of swallowing and speech rehabilitation sessions demonstrated superior swallowing and speech functional outcomes.

CONCLUSIONS

Although a potentially morbid treatment, TGLP and free flap reconstruction can provide good swallowing and speech outcomes as well as meaningful long-term quality of life. Regular attendance of rehabilitation sessions is imperative to optimize functional outcomes.

Systematic evaluation of obstructive sleep apnea websites on the internet

OBJECTIVE

To determine the quality and comprehensiveness of the websites on the Internet with information directed toward patients with obstructive sleep apnea (OSA).

DESIGN

Systematic evaluation of websites on the Internet with information on OSA.

SETTING

World Wide Web.

METHODS

The search engine Google was queried with the term "obstructive sleep apnea." The first 50 results were evaluated. Only websites written in English and containing original information were reviewed.

MAIN OUTCOME MEASURES

A data quality score (DQS) was generated by evaluating each website for the presence of 67 points of information relating to OSA. Each website was also evaluated using a Global Quality Score (GQS), the DISCERN instrument, the Flesch-Kincaid reading grade level, date of the last update, and sources of funding.

RESULTS

Thirty-four websites met the inclusion criteria. The average DQS was 36 points (range 17-57). The average GQS was 2.9 (range 1-5). The average DISCERN score was 3.3 (range 1.9-4.7). The average reading grade level was 11.0 (range 5.0-15.8). Twenty-six websites (76%) provided authorship information. Twenty-five websites (74%) displayed a date of the last update. Of these, 12 websites were not updated within the past 2 years. Twenty websites (59%) provided a source of funding.

CONCLUSIONS

There is a heterogeneous mixture of websites with varying quality on the Internet with information regarding OSA. Health care providers should be cognizant of the variety of information available for patients and be prepared to direct patients toward the high-quality information sources.

Pediatric inferior turbinoplasty with or without adenoidectomy: preliminary report on improvement of quality of life, symptom control, and safety

OBJECTIVE

To determine quality of life (QOL) improvement, symptom control, and safety after inferior turbinoplasty (IT) with or without adenoidectomy (Ad) in children.

DESIGN

Retrospective uncontrolled cohort study.

SETTING

Tertiary care pediatric hospital.

METHODS

A prospective database was searched. The database contained information regarding age, gender, other diagnoses, and complications. Inclusion criteria were (1) children who presented with chronic rhinitis (CR) refractory to medical treatment and (2) children who underwent IT with or without Ad.

MAIN OUTCOME MEASURES

The Glasgow Children's Benefit Inventory (GCBI) was used to assess QOL improvement. The GCBI calculates a score ranging from -100 (maximum harm) to +100 (maximum benefit), with 0 representing no change after surgery.

RESULTS

Eighty-seven patients were identified. Forty-one were excluded owing to concurrent lingual tonsillectomy or septal or sinus surgery. Forty-six consecutive patients were included. Data were obtained from all 46 patients (100%). The average age was 10 years, with 15 females and 31 males. One complication required admission. The GCBI scores showed that patients derived benefit in all domains (median GCBI 28.1, range -6.3 to 93.8).

CONCLUSION

Preliminary results indicate that IT with or without Ad is a safe, beneficial procedure for CR in children. The impact of IT on QOL is comparable to that of well-established operations in otolaryngology.

Systematic review of the quality of patient information on the internet regarding inflammatory bowel disease treatments

BACKGROUND & AIMS

Patients use the Internet as a resource for information about their diseases. A systematic review evaluating the quality of information available for inflammatory bowel disease patients on the Internet regarding treatment options was performed.

METHODS

Google was used to identify 50 websites on 3 occasions. A data quality score (DQS) (potential score, 0-76) was developed to evaluate the content of websites that scores patient information on indications, efficacy, and side effects of treatment. Other outcome measures were a 5-point global quality score, a drug category quality score, the DISCERN instrument, a reading grade level score, and information about integrity.

RESULTS

The median DQS was 22, range 0-74, median global quality score was 2.0, and median Flesch-Kincaid reading grade level was 12.0, range 6.9-13.7. Eight websites achieved a global quality score of 4 or 5. The DQS was highly associated with the global quality score (r = 0.82) and the DISCERN instrument (r = 0.89). There was poor association between the DQS and the rank order in all 3 Google searches. Information on funding source (59%) and date of last update (74%) were often lacking.

CONCLUSIONS

There is marked variation in the quality of available patient information on websites about the treatment options for Crohn's disease and ulcerative colitis. Few websites provided high quality information. There is a need for high quality accredited websites that provide patient-oriented information on treatment options, and these sites need to be updated regularly.

Data standards for flow cytometry

Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of large FCM datasets. We are implementing a standardized approach to capturing, analyzing, and disseminating FCM data that will facilitate both more complex analyses and analysis of datasets that could not previously be efficiently studied. Initial work has focused on developing a community-based guideline for recording and reporting the details of FCM experiments. Open source software tools that implement this standard are being created, with an emphasis on facilitating reproducible and extensible data analyses. As well, tools for electronic collaboration will assist the integrated access and comprehension of experiments to empower users to collaborate on FCM analyses. This coordinated, joint development of bioinformatics standards and software tools for FCM data analysis has the potential to greatly facilitate both basic and clinical research--impacting a notably diverse range of medical and environmental research areas.

A systematic review of patient inflammatory bowel disease information resources on the World Wide Web

BACKGROUND AND AIMS

The Internet is a widely used information resource for patients with inflammatory bowel disease, but there is variation in the quality of Web sites that have patient information regarding Crohn's disease and ulcerative colitis. The purpose of the current study is to systematically evaluate the quality of these Web sites.

METHODS

The top 50 Web sites appearing in Google using the terms "Crohn's disease" or "ulcerative colitis" were included in the study. Web sites were evaluated using a (a) Quality Evaluation Instrument (QEI) that awarded Web sites points (0-107) for specific information on various aspects of inflammatory bowel disease, (b) a five-point Global Quality Score (GQS), (c) two reading grade level scores, and (d) a six-point integrity score.

RESULTS

Thirty-four Web sites met the inclusion criteria, 16 Web sites were excluded because they were portals or non-IBD oriented. The median QEI score was 57 with five Web sites scoring higher than 75 points. The median Global Quality Score was 2.0 with five Web sites achieving scores of 4 or 5. The average reading grade level score was 11.2. The median integrity score was 3.0.

CONCLUSIONS

There is marked variation in the quality of the Web sites containing information on Crohn's disease and ulcerative colitis. Many Web sites suffered from poor quality but there were five high-scoring Web sites.