Double Trouble: How Microbiome Dysbiosis and Mitochondrial Dysfunction Drive Non-Alcoholic Fatty Liver Disease and Non-Alcoholic Steatohepatitis.

Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are closely related liver conditions that have become more prevalent globally. This review examines the intricate interplay between microbiome dysbiosis and mitochondrial dysfunction in the development of NAFLD and NASH. The combination of these two factors creates a synergistic situation referred to as "double trouble", which promotes the accumulation of lipids in the liver and the subsequent progression from simple steatosis (NAFLD) to inflammation (NASH). Microbiome dysbiosis, characterized by changes in the composition of gut microbes and increased intestinal permeability, contributes to the movement of bacterial products into the liver. It triggers metabolic disturbances and has anti-inflammatory effects. Understanding the complex relationship between microbiome dysbiosis and mitochondrial dysfunction in the development of NAFLD and NASH is crucial for advancing innovative therapeutic approaches that target these underlying mechanisms.

Horizon scanning the application of probiotics for wildlife.

The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.

Mycobiome structure does not affect field litter decomposition in Eucalyptus and Acacia plantations.

Mixed tree plantations have been studied because of their potential to improve biomass production, ecosystem diversity, and soil quality. One example is a mixture of Eucalyptus and Acacia trees, which is a promising strategy to improve microbial diversity and nutrient cycling in soil. We examined how a mixture of these species may influence the biochemical attributes and fungal community associated with leaf litter, and the effects on litter decomposition. We studied the litter from pure and mixed plantations, evaluating the effects of plant material and incubation site on the mycobiome and decomposition rate using litterbags incubated in situ. Our central hypothesis was litter fungal community would change according to incubation site, and it would interfere in litter decomposition rate. Both the plant material and the incubation locale significantly affected the litter decomposition. The origin of the litter was the main modulator of the mycobiome, with distinct communities from one plant species to another. The community changed with the incubation time but the incubation site did not influence the mycobiome community. Our data showed that litter and soil did not share the main elements of the community. Contrary to our hypothesis, the microbial community structure and diversity lacked any association with the decomposition rate. The differences in the decomposition pattern are explained basically as a function of the exchange of nitrogen compounds between the litter.

Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE).

In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been recently successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.

Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment.

Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.

Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.

The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.

Harnessing the microbiome to prevent global biodiversity loss.

Global biodiversity loss and mass extinction of species are two of the most critical environmental issues the world is currently facing, resulting in the disruption of various ecosystems central to environmental functions and human health. Microbiome-targeted interventions, such as probiotics and microbiome transplants, are emerging as potential options to reverse deterioration of biodiversity and increase the resilience of wildlife and ecosystems. However, the implementation of these interventions is urgently needed. We summarize the current concepts, bottlenecks and ethical aspects encompassing the careful and responsible management of ecosystem resources using the microbiome (termed microbiome stewardship) to rehabilitate organisms and ecosystem functions. We propose a real-world application framework to guide environmental and wildlife probiotic applications. This framework details steps that must be taken in the upscaling process while weighing risks against the high toll of inaction. In doing so, we draw parallels with other aspects of contemporary science moving swiftly in the face of urgent global challenges.

Paenibacillus piscarius sp. nov., a novel nitrogen-fixing species isolated from the gut of the armored catfish Parotocinclus maculicauda.

A Gram-positive, nitrogen-fixing and endospore-forming strain, designated P121T, was isolated from the gut of the armored catfish (Parotocinclus maculicauda) and identified as a member of the genus Paenibacillus based on the sequences of the 16S rRNA encoding gene, rpoB, gyrB and nifH genes and phenotypic analyses. The most closely related species to strain P121T were Paenibacillus rhizoplanae DSM 103993T, Paenibacillus silagei DSM 101953T and Paenibacillus borealis DSM 13188T, with similarity values of 98.9, 98.3 and 97.6%, respectively, based on 16S rRNA gene sequences. Genome sequencing revealed a genome size of 7,513,698 bp, DNA G + C content of 53.9 mol% and the presence of the structural nitrogenase encoding genes (nifK, nifD and nifH) and of other nif genes necessary for nitrogen fixation. Digital DNA-DNA hybridization (dDDH) experiments and average nucleotide identity (ANI) analyses between strain P121T and the type strains of the closest species demonstrated that the highest values were below the thresholds of 70% dDDH (42.3% with P. borealis) and 95% ANI (84.28% with P. silagei) for bacterial species delineation, indicating that strain P121T represents a distinct species. Its major cellular fatty acid was anteiso-C15:0 (42.4%), and the major isoprenoid quinone was MK-7. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain P121T represents a novel species for which the name Paenibacillus piscarius sp. nov. is proposed (type strain = DSM 25072 = LFB-Fiocruz 1636).

Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica.

Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.

Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica.

Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.

Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality.

Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed "post-heat stress disorder" was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.

Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil.

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems.

Mangrove ecosystems provide important ecological benefits and ecosystem services, including carbon storage and coastline stabilization, but they also suffer great anthropogenic pressures. Microorganisms associated with mangrove sediments and the rhizosphere play key roles in this ecosystem and make essential contributions to its productivity and carbon budget. Understanding this nexus and moving from descriptive studies of microbial taxonomy to hypothesis-driven field and lab studies will facilitate a mechanistic understanding of mangrove ecosystem interaction webs and open opportunities for microorganism-mediated approaches to mangrove protection and rehabilitation. Such an effort calls for a multidisciplinary and collaborative approach, involving chemists, ecologists, evolutionary biologists, microbiologists, oceanographers, plant scientists, conservation biologists, and stakeholders, and it requires standardized methods to support reproducible experiments. Here, we outline the Mangrove Microbiome Initiative, which is focused around three urgent priorities and three approaches for advancing mangrove microbiome research.

High incidence of acquiring methicillin-resistant Staphylococcus aureus in Brazilian children with Atopic Dermatitis and associated risk factors.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) colonization in Atopic Dermatitis (AD) patients can contribute to worsening their clinical condition. OBJECTIVE: A cohort study was carried out to determine the incidence of MRSA acquisition and its risk factors in AD children. METHODS: Patients with AD (2 months-14 years old) were followed up for about 1 year at a reference center for AD treatment in Rio de Janeiro, Brazil, from September 2011 to February 2014. Nasal swabs from patients and contacts were collected every 2 months. The SCORAD system assessed the severity of the AD. S. aureus isolates were evaluated to determine the methicillin resistance and the clonal lineages. RESULTS: Among 117 AD patients, 97 (82.9%) were already colonized with S. aureus and 26 (22.2%) had MRSA at the first evaluation. The incidence of MRSA acquisition in the cohort study was 27.47% (n = 25). The SCORAD assessments were: mild (46.15%), moderate (37.36%) or severe (16.48%). Risk factors were: colonized MRSA contacts (HR = 2.27; 95% CI: 1.16-7.54), use of cyclosporine (HR = 5.84; 95% CI: 1.70-19.98), moderate or severe AD (HR = 3.26; 95% CI: 1.13-9.37). Protective factors were: availability of running water (HR = 0.21; 95% CI: 0.049-0.96) and use of antihistamines (HR = 0.21; 95% IC: 0.64-0.75). MRSA isolates carried the SCCmec type IV and most of them were typed as USA800/ST5. CONCLUSIONS: The high incidence of MRSA acquisition found among AD patients and the risk factors associated show that an effective surveillance of MRSA colonization in these patients is needed.

Inevitable future: space colonization beyond Earth with microbes first.

Based on modern microbiology, we propose a major revision in current space exploration philosophy and planetary protection policy, especially regarding microorganisms in space. Mainly, microbial introduction should not be considered accidental but inevitable. We hypothesize the near impossibility of exploring new planets without carrying and/or delivering any microbial travelers. In addition, although we highlight the importance of controlling and tracking such contaminations-to explore the existence of extraterrestrial microorganisms-we also believe that we must discuss the role of microbes as primary colonists and assets, rather than serendipitous accidents, for future plans of extraterrestrial colonization. This paradigm shift stems partly from the overwhelming evidence of microorganisms' diverse roles in sustaining life on Earth, such as symbioses and ecosystem services (decomposition, atmosphere effects, nitrogen fixation, etc.). Therefore, we propose a framework for new discussion based on the scientific implications of future colonization and terraforming: (i) focus on methods to track and avoid accidental delivery of Earth's harmful microorganisms and genes to extraterrestrial areas; (ii) begin a rigorous program to develop and explore 'Proactive Inoculation Protocols'. We outline a rationale and solicit feedback to drive a public and private research agenda that optimizes diverse organisms for potential space colonization.

Adaptable mesocosm facility to study oil spill impacts on corals.

Although numerous studies have been carried out on the impacts of oil spills on coral physiology, most have relied on laboratory assays. This scarcity is partly explained by the difficulty of reproducing realistic conditions in a laboratory setting or of performing experiments with toxic compounds in the field. Mesocosm systems provide the opportunity to carry out such studies with safe handling of contaminants while reproducing natural conditions required by living organisms. The mesocosm design is crucial and can lead to the development of innovative technologies to mitigate environmental impacts. Therefore, this study aimed to develop a mesocosm system for studies simulating oil spills with several key advantages, including true replication and the use of gravity to control flow-through that reduces reliance on pumps that can clog thereby decreasing errors and costs. This adaptable system can be configured to (a) have continuous flow-through; (b) operate as an open or closed system; (c) be fed by gravity; (d) have separate mesocosm sections that can be used for individual and simultaneous experiments; and (e) simulate the migration of oil from ocean oil spills to the nearby reefs. The mesocosm performance was assessed with two experiments using the hydrocoral Millepora alcicornis and different configurations to simulate two magnitudes of oil spills. With few exceptions, physical and chemical parameters remained stable within replicates and within treatments throughout the experiments. Physical and chemical parameters that expressed change during the experiment were still within the range of natural conditions observed in Brazilian marine environments. The photosynthetic potential (Fv/Fm ) of the algae associated with M. alcicornis decreased in response to an 1% crude-oil contamination, suggesting a successful delivery of the toxic contaminant to the targeted replicates. This mesocosm is customizable and adjustable for several types of experiments and proved to be effective for studies of oil spills.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica.

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience.

The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.

Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core.

The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.

Microbial Community Profiling Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and Denaturing Gradient Gel Electrophoresis (DGGE).

In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community. This chapter focuses on two particular techniques, namely, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE), both of which have been widely used in environmental studies and have been successfully used by the authors in the study of the oral microbial communities associated with conditions of health and disease.