How to Obtain and Compare Metagenome-Assembled Genomes.

Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.

Digital Platform for Continuous Monitoring of Patients Using a Smartwatch: Longitudinal Prospective Cohort Study.

BACKGROUND: Since the COVID-19 pandemic, there has been a boost in the digital transformation of the human society, where wearable devices such as a smartwatch can already measure vital signs in a continuous and naturalistic way; however, the security and privacy of personal data is a challenge to expanding the use of these data by health professionals in clinical follow-up for decision-making. Similar to the European General Data Protection Regulation, in Brazil, the Lei Geral de Proteção de Dados established rules and guidelines for the processing of personal data, including those used for patient care, such as those captured by smartwatches. Thus, in any telemonitoring scenario, there is a need to comply with rules and regulations, making this issue a challenge to overcome. OBJECTIVE: This study aimed to build a digital solution model for capturing data from wearable devices and making them available in a safe and agile manner for clinical and research use, following current laws. METHODS: A functional model was built following the Brazilian Lei Geral de Proteção de Dados (2018), where data captured by smartwatches can be transmitted anonymously over the Internet of Things and be identified later within the hospital. A total of 80 volunteers were selected for a 24-week follow-up clinical trial divided into 2 groups, one group with a previous diagnosis of COVID-19 and a control group without a previous diagnosis of COVID-19, to measure the synchronization rate of the platform with the devices and the accuracy and precision of the smartwatch in out-of-hospital conditions to simulate remote monitoring at home. RESULTS: In a 35-week clinical trial, >11.2 million records were collected with no system downtime; 66% of continuous beats per minute were synchronized within 24 hours (79% within 2 days and 91% within a week). In the limit of agreement analysis, the mean differences in oxygen saturation, diastolic blood pressure, systolic blood pressure, and heart rate were -1.280% (SD 5.679%), -1.399 (SD 19.112) mm Hg, -1.536 (SD 24.244) mm Hg, and 0.566 (SD 3.114) beats per minute, respectively. Furthermore, there was no difference in the 2 study groups in terms of data analysis (neither using the smartwatch nor the gold-standard devices), but it is worth mentioning that all volunteers in the COVID-19 group were already cured of the infection and were highly functional in their daily work life. CONCLUSIONS: On the basis of the results obtained, considering the validation conditions of accuracy and precision and simulating an extrahospital use environment, the functional model built in this study is capable of capturing data from the smartwatch and anonymously providing it to health care services, where they can be treated according to the legislation and be used to support clinical decisions during remote monitoring.

Digital Platform to Continuously Monitor Patients Using a Smartwatch: Preliminary Report.

BACKGROUND: Monitoring vital signs such as oximetry, blood pressure, and heart rate is important to follow the evolution of patients. Smartwatches are a revolution in medicine allowing the collection of such data in a continuous and organic way. However, it is still a challenge to make this information available to health care professionals to make decisions during clinical follow-up. OBJECTIVE: This study aims to build a digital solution that displays vital sign data from smartwatches, collected remotely, continuously, reliably, and from multiple users, with trigger warnings when abnormal results are identified. METHODS: This is a single-center prospective study following the guidelines "Evaluating digital health products" from the UK Health Security Agency. A digital platform with 3 different applications was created to capture and display data from the mobile phones of volunteers with smartwatches. We selected 80 volunteers who were followed for 24 weeks each, and the synchronization interval between the smartwatch and digital solution was recorded for each vital sign collected. RESULTS: In 14 weeks of project progress, we managed to recruit 80 volunteers, with 68 already registered in the digital solution. More than 2.8 million records have already been collected, without system downtime. Less than 5% of continuous heart rate measurements (bpm) were synchronized within 2 hours. However, approximately 70% were synchronized in less than 24 hours, and 90% were synchronized in less than 119 hours. CONCLUSIONS: The digital solution is working properly in its role of displaying data collected from smartwatches. Vital sign values are being monitored by the research team as part of the monitoring of volunteers. Although the digital solution proved unsuitable for monitoring urgent events, it is more than suitable for use in outpatient clinical use. This digital solution, which is based on cloud technology, can be applied in the future for telemonitoring in regions lacking health care professionals. Accuracy and reliability studies still need to be performed at the end of the 24-week follow-up.

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions.

BACKGROUND: Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. RESULTS: Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. CONCLUSIONS: The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

Background Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Results Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. Conclusions The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.