A Set of In Situ Informed Simulated Medium Formats for Culturing Environmentally Acquired Anaerobic Microorganisms.

Culture-dependent research of anaerobic microorganisms rests upon methodological competence. These methods must create and maintain suitable growth conditions (e.g., pH and carbon sources) for anaerobic microorganisms while also allowing samples to be extracted without compromising the artificial environment. To this end, methods that are informed by and simulate an in situ environment can be of great aid in culturing microorganisms from that environment. Here, we outline an in situ informed and simulated anaerobic method for culturing terrestrial surface and subsurface microorganisms, emphasizing anaerobic sample collection with minimal perturbation. This protocol details the production of a customizable anaerobic liquid medium, and the environmental acquisition and in vitro growth of anaerobic microorganisms. The protocol also covers critical components of an anaerobic bioreactor used for environmental simulations of sediment and anaerobic liquid media for environmentally acquired cultures. We have included preliminary Next Generation Sequencing data from a maintained microbiome over the lifespan of a bioreactor where the active culture dynamically adjusted in response to an experimental carbon source.

Aquaculture production of hatchling Hawaiian Bobtail Squid (Euprymna scolopes) is negatively impacted by decreasing environmental microbiome diversity.

AIMS: The Hawaiian Bobtail Squid (Euprymna scolopes) is a model organism for investigating host-symbiont relationships. The current scientific focus is on the microbiome within E. scolopes, while very little is known about the microbiome of the tanks housing E. scolopes. We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid. METHODS AND RESULTS: Total DNA was extracted from sediment and filtered water samples from 'productive' squid cohorts with high embryonic survival and paralarval hatching, 'unproductive' cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where E. scolopes is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty-eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included Aquicella, Woeseia and Ferruginibacter, with Hyphomicrobium and Rhizohapis were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate-reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels. CONCLUSIONS: We conclude that microbiome composition and water geochemistry can negatively affect E. scolopes reproductive physiology in closed tank systems, ultimately impacting host-microbe research using these animals. SIGNIFICANCE AND IMPACT OF STUDY: These results identify the tight relationship between the microbiome and geochemistry to E. scolopes. From this study, it may be possible to design probiotic counter-measures to improve aquaculture conditions for E. scolopes.

Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T.

BACKGROUND: There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS: The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS: The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.

HSV Hepatitis in Pregnancy: A Review of the Literature.

IMPORTANCE: Herpes simplex virus (HSV) hepatitis is a rare condition with a high mortality rate. Immunocompromised individuals, including pregnant women, are the most susceptible. When primary infection occurs during pregnancy, risk for disseminated HSV is greatly increased. Disseminated HSV can manifest in the form of HSV hepatitis. OBJECTIVE: We aim to review the literature and summarize what is known about HSV hepatitis in pregnancy to aid in the diagnosis and treatment of this condition. EVIDENCE ACQUISITION: A literature search of PubMed and Web of Science was performed. A total of 237 citations were found. All citations were independently reviewed. Thirty-eight full-text articles were identified and included in this review. Additional data from 1 unpublished case from our institution was included. RESULTS: Fifty-six cases were included with average gestational age at diagnosis of 30 weeks. Patients presented with a wide variety of gastrointestinal, respiratory, neurologic, and urogenital symptoms. The most common examination findings were fever and abdominal tenderness. Only 18.2% of patients had a vesicular rash. All patients had a transaminitis, and 85% had positive viral cultures. A multitude of treatments were used with the majority of favorable outcomes occurring after treatment with acyclovir. CONCLUSIONS AND RELEVANCE: Although HSV hepatitis is rare, it carries a mortality rate of up to 39% for mothers and neonates. Therefore, it is crucial that HSV hepatitis be included on the differential diagnosis when a patient presents with fever and transaminitis. When HSV hepatitis is suspected, empiric therapy with acyclovir can be initiated with no additional risk to the fetus.

Complications of ERCP for choledocholithiasis in a sickle cell cohort.

BACKGROUND: Patients with sickle cell disease (SCD) demand special attention during clinical interventions because they are predisposed to acute chest syndrome (ACS), vaso-occlusive crises, intra-vascular haemolysis and immune paresis. Although SCD is endemic in the Caribbean, there has been no report on endoscopic retrograde cholangio-pancreatography (ERCP) outcomes in these patients from this region. STUDY: The records of patients with SCD who underwent ERCP between 1 January 2005 and 1 June 2010 were analysed retrospectively. Parameters assessed included patient demographics, procedural details, ERCP-related and SCD-related morbidity. Data were analysed using SPSS version 12.0. RESULTS: Fifty-four patients with SCD were subjected to ERCP during the study period. There were 37 women and 17 men at a mean age of 28 years (SD +/-12.05). There was 29% (16) overall morbidity, with 10 (18.5%) SCD-related complications and six (11.1%) ERCP-specific complications. More common complications were: pancreatitis (9.3%); cholangitis (1.9%); ACS (9.3%); pneumonia (3.7%); and painful crises (5.6%). There was one death (1.9%) due to multiple organ failure secondary to severe pancreatitis. CONCLUSIONS: This study suggests that the SCD cohort requires special perioperative attention to minimise the inordinately high morbidity, many of which are SCD-related. We propose a perioperative management protocol that may minimise morbidity in these patients.

Overcoming obstacles to establish a multidisciplinary team approach to hepatobiliary diseases: a working model in a Caribbean setting.

INTRODUCTION: By providing a structured forum to exchange information and ideas, multidisciplinary team meetings improve working relationships, expedite investigations, promote evidence-based treatment, and ultimately improve clinical outcomes. METHODS: This discursive paper reports the introduction of a multidisciplinary team approach to manage hepatobiliary diseases in Jamaica, focusing on the challenges encountered and the methods used to overcome these obstacles. CONCLUSION: Despite multiple challenges in resource-limited environments, a multidisciplinary team approach can be incorporated into clinical practice in developing nations. Policy makers should make it a priority to support clinical, operational, and governance aspects of the multidisciplinary teams.

Endoscopic transmural drainage of pancreatic pseudocysts: technical challenges in the resource poor setting.

Although surgical drainage of pancreatic pseudocysts has been superseded by less invasive options, the requirement for specialized equipment, technical expertise, and consumables limits the options available in low resource settings. We describe the challenges experienced during endoscopic transmural drainage in a low resource setting and the methods used to overcome these barriers. Despite operating in a low resource environment, endoscopic drainage of pancreatic pseudocysts can be incorporated into our armamentarium with minimal change to the existing hardware. Careful patient selection by a dedicated multidisciplinary team should be observed in order to achieve good outcomes.