Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature’s own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.

Ventilator Associated Pneumonia in Pediatric Trauma Patients

Background: Ventilator associated pneumonia (VAP) is a common hospital-acquired infection found in intubated trauma patients. In previous adult studies, VAP has been associated with an increase in length of stay, cost, morbidity, mortality, and longer mechanical ventilation. There remains little examination of the risk factors, prognosis, and microbiology of VAP within the pediatric trauma population. This study aims to analyze factors associated with VAP in pediatric trauma patients. Methods: The Riley Hospital for Children Trauma Registry was utilized to identify intubated pediatric trauma patients from 2016-2020. Patients were excluded if intubated for less than 48 hours. VAP was defined as positive if patients met either Centers for Disease Control definition and or were clinically diagnosed with and treated for VAP. Univariate and multivariate modeling was performed. Results: A total of 171 patients met inclusion criteria and 43 (25%) were diagnosed with VAP. The median age was 8 years (2-13) and ISS was 26.5 (22-35). The median duration of intubation was 203.8 hours (117.3-331.3). The overall mortality was 55 (32.2%). While variables such as lower age and use of MTP resulted in a higher likelihood of mortality, VAP diagnosis was not associated with increased mortality. BAL analysis displayed that the most common cultured bacteria were H. influenzae, Staph. aureus, and Strep. Pneumoniae with most VAPs being diagnosed on day 2 of admission. When analyzing the impact of age, ISS, intubation hours, ICU days, and GI prophylaxis on VAP, only age was significantly associated with VAP: for each year the odds of VAP rose by 10%. Conclusions: A quarter of the pediatric trauma patients were diagnosed with VAP during the study period. No modifiable risk factors were found for VAP with only patient age demonstrating significance for the diagnosis. Further investigation into VAP definition and prevention in pediatric trauma patients should occur given it’s prevalence.

Enhanced Asymptomatic Systemic Infection Caused by Plesiomonas shigelloides in a Captive Gray Wolf (Canis lupus)

A 7-year-old male gray wolf was found dead at a zoo during exhibition. To determine the cause of death, histological and gross necropsy diagnoses and a molecular analysis were performed. The gross necropsy revealed a swollen abdomen, hemorrhagic exudates around the mouth, splenomegaly, a discolored liver, a congested kidney, hemorrhagic ascites, and dark gray-colored membranes and air bubbles in the fundus of the stomach. Rod-shaped bacteria were found in the liver parenchyma and hemorrhagic ascites using Giemsa staining. The nucleotide sequencing of the cultured bacteria identified the causative agent as Plesiomonas shigelloides, which is rarely responsible for systemic infections. This study describes a rare case and the first reported systemic gastrointestinal infection due to P. shigelloides in a zoo animal.

Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion

Microbial contamination of fuels, associated with a wide variety of bacteria and fungi, leads to decreased product quality and can compromise equipment performance by biofouling or microbiologically influenced corrosion. Detection and quantification of microorganisms are critical in monitoring fuel systems for an early detection of microbial contaminations. To address these challenges, we have analyzed six metagenomes, one transcriptome, and more than 1,200 fluid and swab samples taken from fuel tanks or kerosene. Our deep metagenome sequencing and binning approaches in combination with RNA-seq data and qPCR methods implied a metabolic symbiosis between fungi and bacteria. The most abundant bacteria were affiliated with α-, β-, and γ-Proteobacteria and the filamentous fungi Amorphotheca. We identified a high number of genes, which are related to kerosene degradation and biofilm formation. Surprisingly, a large number of genes coded enzymes involved in polymer degradation and potential bio-corrosion processes. Thereby, the transcriptionally most active microorganisms were affiliated with the genera Methylobacteria, Pseudomonas, Kocuria, Amorpotheka, Aspergillus, Fusarium, and Penicillium. Many not yet cultured bacteria and fungi appeared to contribute to the biofilm transcriptional activities. The largest numbers of transcripts were observed for dehydrogenase, oxygenase, and exopolysaccharide production, attachment and pili/flagella-associated proteins, efflux pumps, and secretion systems as well as lipase and esterase activity.

Human Gut Microbial Taxa Metabolizing Dietary Obesogens: A BPA 1 directed-culturing and Bioinformatics Combined Approach

Background Integrated data from culturomics and functional omics may depict holistic understanding on gut microbiome eubiosis or dysbiosis, and microbial isolates can become a source of differential enzymes and useful bioactive compounds. Culturing methods developed during last decade swift increases the importance of gut microbial isolates, focusing on media, modifications and conditions that propitiate cultured taxa that previously were considered fastidious or unculturable. In this context and focusing on gut microbiota dysbiosis triggered by obesogens and microbiota disrupting chemicals (MDC), we have conducted a directed-culturing and bioinformatics combined approach, adding bisphenol A (BPA) and specific treatments to find resistant spore-forming bacteria, to obtain isolated strains for further explore their molecular BPA metabolizing or neutralizing capacities. Results Overall microbiota culturing media and conditions have been retrieved and organized according to main gut taxa isolated during last decade. Furthermore, a catalogue of BPA directed-cultured microorganisms has been obtained from 46 fecal samples from two populations, children with obesity and normo-weight. A total of 235 BPA tolerating and potentially BPA biodegrading microorganisms were mainly grouped to strictly anaerobic sporuled/non-sporuled, anaerobic facultative sporuled/non-sporuled. Firmicutes, Enterobacteria and Actinobacteria species showed the major representation in both groups. However, differential BPA tolerant microbiota composition from the populations was detected. Bioinformatics analysis disclosed and predicted the variability of harboring genes encoding specific enzyme for BPA biodegradation pathways that corroborated from directed-culturing microbiota consortia obtained. Conclusions Strains from Staphylococcus , Bacillus and Enterococcus genera represented the majority of the successfully cultured bacteria in both population specimens. From them, the bioinformatics prediction assigned to Bacillus spp. the higher potential for BPA biodegradation. Therefore, extensive directed-culturomics approaches could be designed for different MDC with common biodegradation pathways, such as parabens, phthalates, and benzophenones.

IDENTIFIKASI DAN UJI SENSITIVITAS BAKTERI Neisseria gonorrhoeae TERHADAP ANTIBIOTIK SEFIKSIM PADA PEKERJA SEKS KOMERSIAL DI PUSKESMAS II DENPASAR SELATAN

Gonorrhea is a sexually transmitted disease caused by Neisseria gonorrhoeae. Gonorrhea infection varies greatly in the community, especially in sexually active women. Infection cases in women are often asymptomatic, that can causes complication can easily occur. The aims of this study are to identify and determine sensitivity of Neisseria gonorrhoeae bacteria against cefixime antibiotics. This study was using a descriptive method and used 30 samples. Neisseria gonorrhoeae was isolatd from the vaginal swab sample of Commercial Sex Workers at Puskesmas II Denpasar Selatan. The cultured bacteria on Thayer Martin media were then identified by gram staining, oxidase test, and catalase test. Neisseria gonorrhoeae sensitivity test against cefixime was performed by disc diffusion method. The results of identification showed that 6 (20 %) of 30 samples were Neisseria gonorrhoeae bacteria with cell characteristics in the form of diplococcus, gram-negative, oxidase and catalase positive. The results of the sensitivity test showed that all isolats of Neisseria gonorrhoeae were resistant to cefixime

A metabolomics pipeline enables mechanistic interrogation of the gut microbiome

Gut microbes modulate host phenotypes and are associated with numerous health effects in humans, ranging from cancer immunotherapy response to metabolic disease and obesity. However, difficulty in accurate and high-throughput functional analysis of human gut microbes has hindered defining mechanistic connections between individual microbial strains and host phenotypes. One key way the gut microbiome influences host physiology is through the production of small molecules1-3, yet progress in elucidating this chemical interplay has been hindered by limited tools calibrated to detect products of anaerobic biochemistry in the gut. Here we construct a microbiome-focused, integrated mass-spectrometry pipeline to accelerate the identification of microbiota-dependent metabolites (MDMs) in diverse sample types. We report the metabolic profiles of 178 gut microbe strains using our library of 833 metabolites. Leveraging this metabolomics resource we establish deviations in the relationships between phylogeny and metabolism, use machine learning to discover novel metabolism in Bacteroides, and employ comparative genomics-based discovery of candidate biochemical pathways. MDMs can be detected in diverse biofluids in gnotobiotic and conventional mice and traced back to corresponding metabolomic profiles of cultured bacteria. Collectively, our microbiome-focused metabolomics pipeline and interactive metabolomics profile explorer are a powerful tool for characterizing microbe and microbe-host interactions.

BACTERIAL ISOLATES AND ANTIBIOTIC SENSITIVITY PATTERNS IN CHOLEDOCHAL BILE COLLECTED DURING ERCP: A REPORT FROM CENTRAL INDIA.

Temporal shifts have been known to occur in antibiotic sensitivity patterns of organisms causing cholangitis.The aim of this prospective study conducted on 100 patients of extra hepatic biliary obstruction (EHBO) was to identify the common microorganisms cultured from bile obtained during Endoscopic retrograde cholangiography and to study their local sensitivity pattern.Sixty six patients had growth in bile culture,the maximum growths amongst all micro-organisms were of Escherichia coli (40.9%) and Pseudomonas aeruginosa (40.9%). Growth rates were significantly higher in patients with non- malignant causes of biliary obstruction than those with malignant causes. Polymixins had the highest sensitivity to cultured bacteria followed by aminoglycosides and Imipenem.Study of culture & sensitivity pattern helps in deciding empirical antibiotic therapy in patients with cholangitis and it should be based on local sensitivity patterns

Biodegradation Study of Potato Starch-based Bioplastic

Background: Plastics are indispensable for our society. The extensive use of petroleum-based plastic and dumping of the same in soil and water body greatly affects our environment and biodiversity. However, biodegradable plastics can reduce the volume of waste in packaging materials. Therefore, biomass-derived polymers are promising alternatives of the petroleum-based non-degradable polymer to address the environmental issues. Objective: A large number of reports on the synthesis and characterization of starch-based bioplastic are available in the literature. However, a detailed biodegradation study of the starch-based bioplastic is rarely reported. We have prepared potato starch-based bioplastic with the combination of various plasticizers (glycerol, sorbitol, and xylitol) through hydrogel formation and carried out their biodegradation study. Method: Present study investigated the biodegradation of potato starch-based bioplastic in the natural environment, in cultured bacteria, and with fungal α-amylase. Results: Starch-based plastic is completely degraded in the natural environment within two months. Bacteria culture in solid media resulted in various types of bacterial colonies. Among the various bacterial colonies, the white circular colony was the major bacteria that degrade starch-based plastic. Furthermore, we screened the starch-based plastic degrading bacteria and isolated the pure culture through the streak plate method. Conclusion: n presence of cultured bacteria and with fungal α-amylase, starch-based plastic is completely degraded within 96h and 48h respectively.