Coracle-a machine learning framework to identify bacteria associated with continuous variables.

SUMMARY: We present Coracle, an artificial intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e. bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e. 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e. standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g. order or family) to identify groups of interest that can subsequently be run at the ASV level. AVAILABILITY AND IMPLEMENTATION: Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git.

Mitigating the ecological collapse of coral reef ecosystems: Effective strategies to preserve coral reef ecosystems: Effective strategies to preserve coral reef ecosystems.

Global warming is decimating coral reefs. We need to implement mitigation and restoration strategies now to prevent coral reefs from disappearing altogether.

Hurdles and opportunities in implementing marine biosecurity systems in data-poor regions.

Managing marine nonindigenous species (mNIS) is challenging, because marine environments are highly connected, allowing the dispersal of species across large spatial scales, including geopolitical borders. Cross-border inconsistencies in biosecurity management can promote the spread of mNIS across geopolitical borders, and incursions often go unnoticed or unreported. Collaborative surveillance programs can enhance the early detection of mNIS, when response may still be possible, and can foster capacity building around a common threat. Regional or international databases curated for mNIS can inform local monitoring programs and can foster real-time information exchange on mNIS of concern. When combined, local species reference libraries, publicly available mNIS databases, and predictive modeling can facilitate the development of biosecurity programs in regions lacking baseline data. Biosecurity programs should be practical, feasible, cost-effective, mainly focused on prevention and early detection, and be built on the collaboration and coordination of government, nongovernment organizations, stakeholders, and local citizens for a rapid response.

Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals.

Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral-associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin-repeat protein A and internalin B, which indirectly cause histone modifications in humans, as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral-associated bacteria indicate that there are potential host epigenome-modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4.

Neovaginoplasty With Nile Tilapia Skin: Cytological and Microbiota Evaluation.

OBJECTIVES: To study the clinical, cytological, and vaginal microbiota findings in patients with Mayer-Rokitansky-Küster-Hauser syndrome who underwent neovaginoplasty using Nile tilapia fish skin. METHODS: This is a cross-sectional study with 7 cisgender women with Mayer-Rokitansky-Küster-Hauser syndrome who had previously undergone neovagina reconstruction using Nile tilapia fish skin at a university hospital. Local institutional review board approval and written permission from the patient were obtained. Between August 2019 and November 2021, within 12 to 24 months after surgery, vaginal specimens were obtained for conventional oncotic and hormonal cytology, and for Gram staining. The Nugent scores were calculated. Colposcopy was also performed. RESULTS: Squamous cells without atypia were found in all patients. Five patients had intermediate vaginal microbiota (Nugent score of 4), which was determined by the presence of few lactobacilli on Gram staining. In hormonal cytology, 4 patients presented with findings compatible with menacme. No colposcopic change was observed. When postsurgical dilation was performed correctly, a mean vaginal length of 8.3 cm was maintained after 1 year of follow-up. CONCLUSIONS: Squamous cells without atypia were present in neovaginas with Nile tilapia fish skin. Most vaginal contents revealed intermediate microbiota and hormonal results compatible with menacme. Studies with a greater number of patients are necessary for a more comprehensive understanding of the microbiome in neovaginas with this new technique, thereby providing support for the treatment and prevention of associated pathologies.

Host-associated microbiomes drive structure and function of marine ecosystems.

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.

Continuation and satisfaction with intrauterine copper device inserted during caesarean delivery.

PURPOSE: The objective was to assess the continuation and satisfaction of women who had copper IUDs inserted during caesarean delivery, in addition to possible factors associated with device positioning. MATERIALS AND METHODS: A prospective, observational study was carried out involving 158 women who underwent copper IUD insertion during caesarean delivery in Fortaleza, Brazil. The women were followed up 6 weeks and 6 months after insertion of the IUD, at which time they completed a satisfaction questionnaire. We performed speculum and ultrasound examination. RESULTS: IUD continuation rates after 6 weeks and 6 months were 92% and 71.5%, respectively. Approximately 85% and 76% of the women were satisfied with the method after 6 weeks and 6 months, respectively. The rate of poor positioning on ultrasound was 5% and the rate of visible thread after 6 weeks was 29.1%, both without association with age, parity, gestational age or active labour. There were 2 cases of infection (1.3%) and no cases of perforation or pregnancy. CONCLUSIONS: There was a good rate of continuation and satisfaction with the immediate post-caesarean IUD. There was no association between IUD malpositioning and age, parity, gestational age or active labour.

The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.

Eucalyptus plantations offer a cost-effective and renewable source of raw material. There is substantial interest in improving forestry production, especially through sustainable strategies such as the use of plant growth-promoting bacteria. However, little is known about Eucalyptus microbiology. In this study, the endophytic bacterial community was assessed in Eucalyptus urograndis roots using culture-dependent and culture-independent techniques with plants grown under different conditions. Three phyla accounted for approximately 95% of the community, with Actinobacteria corresponding to approximately 59%. This contrasts with previous studies in which Actinobacteria accounted for only 5 to 10%. Our data also revealed a high diversity of bacteria, with 359 different genera but a high level of dominance. Six genera, Mycobacterium, Bradyrhizobium, Streptomyces, Bacillus, Actinospica, and Burkholderia, accounted for more than 50% of the classified sequences. We observed a significant influence of the treatments on some genera, causing changes in the bacterial community structure. The obtained data also suggest that Eucalyptus may benefit from biological nitrogen fixation, with many abundant genera being closely related to nitrogen-fixing bacteria. Using N-depleted media, we also cultured 95 bacterial isolates, of which 24 tested positive for the nifH gene and were able to maintain growth without any N source in the medium.

Correction to: The Microbiome of Eucalyptus Roots under Different Management Conditions and Its Potential for Biological Nitrogen Fixation.

The original version of this article unfortunately contained mistakes in the first author's name and the running page headers.

Antarctic strict anaerobic microbiota from Deschampsia antarctica vascular plants rhizosphere reveals high ecology and biotechnology relevance.

The Antarctic soil microbial community has a crucial role in the growth and stabilization of higher organisms, such as vascular plants. Analysis of the soil microbiota composition in that extreme environmental condition is crucial to understand the ecological importance and biotechnological potential. We evaluated the efficiency of isolation and abundance of strict anaerobes in the vascular plant Deschampsia antarctica rhizosphere collected in the Antarctic's Admiralty Bay and associated biodiversity to metabolic perspective and enzymatic activity. Using anaerobic cultivation methods, we identified and isolated a range of microbial taxa whose abundance was associated with Plant Growth-Promoting Bacteria (PGPB) and presences were exclusively endemic to the Antarctic continent. Firmicutes was the most abundant phylum (73 %), with the genus Clostridium found as the most isolated taxa. Here, we describe two soil treatments (oxygen gradient and heat shock) and 27 physicochemical culture conditions were able to increase the diversity of anaerobic bacteria isolates. Heat shock treatment allowed to isolate a high percentage of new species (63.63 %), as well as isolation of species with high enzymatic activity (80.77 %), which would have potential industry application. Our findings contribute to the understanding of the role of anaerobic microbes regarding ecology, evolutionary, and biotechnological features essential to the Antarctic ecosystem.

Cyanobacterial and microeukaryotic profiles of healthy, diseased, and dead Millepora alcicornis from the South Atlantic.

Coral reefs are at risk due to events associated with human activities, which have resulted in the increasing occurrence of coral diseases. Corals live in symbiotic relationships with different microorganisms, such as cyanobacteria, a very important group. Members of the phylum Cyanobacteria are found in great abundance in the marine environment and may play an essential role in keeping corals healthy but may also be pathogenic. Furthermore, some studies are showing a rise in cyanobacterial abundance in coral reefs as a result of climate change. The current study aimed to improve our understanding of the relationship between cyanobacteria and coral health. Our results revealed that the cyanobacterial genus GPI (Anabaena) is a possible opportunistic pathogen of the coral species Millepora alcicornis in the South Atlantic Ocean. Furthermore, the bacterial and microeukaryotic profile of healthy, diseased, and post-disease (skeletal) regions of affected coral indicated that a microbial consortium composed of Anabaena sp., Prosthecochloris sp., and microeukaryotes could be involved in this pathogenicity or could be taking advantage of the diseased state.

Evaluation of soil bioremediation techniques in an aged diesel spill at the Antarctic Peninsula.

Many areas on the Antarctic continent already suffer from the direct and indirect influences of human activities. The main cause of contamination is petroleum hydrocarbons because this compound is used as a source of energy at the many research stations around the continent. Thus, the current study aims to evaluate treatments for bioremediation (biostimulation, bioaugmentation, and bioaugmentation + biostimulation) using soils from around the Brazilian Antarctic Station "Comandante Ferraz" (EACF), King George Island, Antarctic Peninsula. The experiment lasted for 45 days, and at the end of this period, chemical and molecular analyses were performed. Those analyses included the quantification of carbon and nitrogen, denaturing gradient gel electrophoresis (DGGE) analysis (with gradient denaturation), real-time PCR, and quantification of total hydrocarbons and polyaromatics. Molecular tests evaluated changes in the profile and quantity of the rrs genes of archaea and bacteria and also the alkB gene. The influence of the treatments tested was directly related to the type of soil used. The work confirmed that despite the extreme conditions found in Antarctic soils, the bacterial strains degraded hydrocarbons and bioremediation treatments directly influenced the microbial communities present in these soils even in short periods. Although the majority of the previous studies demonstrate that the addition of fertilizer seems to be most effective at promoting bioremediation, our results show that for some conditions, autochthonous bioaugmentation (ABA) treatment is indicated. This work highlights the importance of understanding the processes of recovery of contaminated environments in polar regions because time is crucial to the soil recovery and to choosing the appropriate treatment.

Detection of proteases from Sporosarcina aquimarina and Algoriphagus antarcticus isolated from Antarctic soil.

Two psychrophilic bacterial samples were isolated from King George Island soil, in Antarctica. The phylogenetic analysis based on the 16S rRNA (rrs) gene led to the correlation with the closest related isolates as Sporosarcina aquimarina (99%) and Algoriphagus antarcticus (99%), with query coverage of 99% and 98%, respectively. The spent culture media from both isolates displayed proteolytic activities detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis containing gelatin as protein substrate. Under the employed conditions, S. aquimarina showed a 55 kDa protease with the best activity detected at pH 7.0 and at 27°C. A. antarcticus also showed a single extracellular protease, however its molecular mass was around 90kDa and its best activity was detected at pH 9.0 and at 37°C. The proteases from both isolates were inhibited by 1,10-phenanthroline and EDTA, two metalloprotease inhibitors. This is the first record of protease detection in both species, and our results may contribute to broaden the basic knowledge of proteases from the Antarctica environment and may help prospecting future biotechnological applications of these enzymes.

Bacterial and Archaeal Communities Variability Associated with Upwelling and Anthropogenic Pressures in the Protection Area of Arraial do Cabo (Cabo Frio region - RJ).

Upwelling systems contain a high diversity of pelagic microorganisms and their composition and activity are defined by factors like temperature and nutrient concentration. Denaturing gradient gel electrophoresis (DGGE) technique was used to verify the spatial and temporal genetic variability of Bacteria and Archaea in two stations of the Arraial do Cabo coastal region, one under upwelling pressure and another under anthropogenic pressure. In addition, biotic and abiotic variables were measured in surface and deep waters from three other stations between these stations. Six samplings were done during a year and adequately represented the degrees of upwelling and anthropogenic pressures to the system. Principal Component Analysis (PCA) showed negative correlations between the concentrations of ammonia and phosphorous with prokaryotic secondary production and the total heterotrophic bacteria. PCA also showed negative correlation between temperature and the abundance of prokaryotic cells. Bacterial and archaeal compositions were changeable as were the oceanographic conditions, and upwelling had a regional pressure while anthropogenic pressure was punctual. We suggest that the measurement of prokaryotic secondary production was associated with both Bacteria and Archaea activities, and that substrate availability and temperature determine nutrients cycling.

Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.

Impact of next generation sequencing techniques in food microbiology.

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.

Choice and factors associated to the use of contraceptive methods among postpartum women: A prospective cohort study.

OBJECTIVES: To assess women's contraceptive preferences in the immediate postpartum period and identify factors associated with use of their desired contraceptive method six months later. MATERIAL AND METHODS: This prospective cohort study included women ≤48 h after delivery at a single public Brazilian hospital. The women's interview took place in two different momentsbefore hospital discharge (in-person interview) and six months after delivery (by telephone contact). For data collection and management, we used the REDCap electronic tool. Univariate and multivariate analyses (unadjusted and adjusted Odds Ratio and 95 % confidence intervals) were used to identify factors associated with higher use of their desired contraceptive method six months after delivery. RESULTS: A total of 294 women (166 adolescents) were included. Initial contraceptive preferences were especially intrauterine devices (IUDs) (39.1 %), implants (33.0 %) and injectable hormonal contraceptives (17.0 %). Six months later, 42.5 % (n = 125) were using their desired contraceptive method. Younger age, white race and contraceptive initiation prior to hospital discharge were associated with use of their desired contraceptive at six months. CONCLUSION: Long-acting reversible contraception (LARC) methods were the most desired contraceptives among women after delivery. Providing and initiating free contraception prior to discharge from a birthing unit is important with regard to use of their desired method.

Unlocking the genomic potential of Red Sea coral probiotics.

The application of beneficial microorganisms for corals (BMC) decreases the bleaching susceptibility and mortality rate of corals. BMC selection is typically performed via molecular and biochemical assays, followed by genomic screening for BMC traits. Herein, we present a comprehensive in silico framework to explore a set of six putative BMC strains. We extracted high-quality DNA from coral samples collected from the Red Sea and performed PacBio sequencing. We identified BMC traits and mechanisms associated with each strain as well as proposed new traits and mechanisms, such as chemotaxis and the presence of phages and bioactive secondary metabolites. The presence of prophages in two of the six studied BMC strains suggests their possible distribution within beneficial bacteria. We also detected various secondary metabolites, such as terpenes, ectoines, lanthipeptides, and lasso peptides. These metabolites possess antimicrobial, antifungal, antiviral, anti-inflammatory, and antioxidant activities and play key roles in coral health by reducing the effects of heat stress, high salinity, reactive oxygen species, and radiation. Corals are currently facing unprecedented challenges, and our revised framework can help select more efficient BMC for use in studies on coral microbiome rehabilitation, coral resilience, and coral restoration.

The coral microbiome in sickness, in health and in a changing world.

Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.