The impact of microbiota and ketogenic diet interventions in the management of drug-resistant epilepsy.

AIM: Drug-resistant epilepsy (DRE) is a neurological disorder characterized by uncontrolled seizures. It affects between 10%-40% of the patients with epilepsy worldwide. Drug-resistant patients have been reported to have a different microbiota composition compared to drug-sensitive patients and healthy controls. Importantly, fecal microbiota transplantations (FMTs), probiotic and dietary interventions have been shown to be able to reduce seizure frequency and improve the quality of life in drug-resistant patients. The classic ketogenic diet (KD) and its modifications may reduce seizures in DRE in some patients, whereas in others they do not. The mechanisms mediating the dietary effects remain elusive, although it is known that gut microbes play an important role in transmitting dietary effects to the host. Indeed, specific commensal microbes differ even between responders and non-responders to KD treatment. METHODS: In this narrative mini-review, we summarize what is known about the gut microbiota changes and ketogenic diets with special focus on patients with DRE. RESULTS AND CONCLUSIONS: By highlighting unanswered questions and by suggesting future research directions, we map the route towards future improvement of successful DRE therapy.

Nutrition during pregnancy: Influence on the gut microbiome and fetal development.

Pregnancy is a finely tuned process, with the health and well-being of the developing fetus determined by the metabolic status and dietary intake of the mother. The maternal gut microbiome is remodeled during pregnancy, and this, coupled with the maternal nutrient intake during gestation shapes the production of metabolites that can cross the placenta and affect fetal development. As posited by the Developmental Origins of Health and Disease Hypothesis, such environmental influences can have major effects on the developing organ systems. When occurring at particularly sensitive gestational time points, these developmental programming events can have long lasting effects on offspring adaptation to the postnatal environment, and major health implications later in life. This review will summarize current knowledge on how pregnancy and maternal dietary intake intrinsically and extrinsically modify maternal gut microbiota composition and metabolite production. Further, we will assess how these factors shape the fetal landscape and ultimately contribute to offspring health. DOHaD, fetal development, metabolites, microbiome, nutrition, pregnancy, short-chain fatty acids.

Microbiota, diet, and the gut-brain axis in multiple sclerosis and stroke.

Intestinal microbiota can influence the phenotype and function of immune cell responses through the dissemination of bacterial antigens or metabolites. Diet is one of the major forces shaping the microbiota composition and metabolism, contributing to host homeostasis and disease susceptibility. Currently, nutrition is a complementary and alternative approach to the management of metabolic and neurological diseases and cancer. However, the knowledge of the exact mechanism of action of diet and microbiota on the gut-brain communication is only developing in recent years. Here, we reviewed the current knowledge on the effect of diet and microbiota on the gut-brain axis in patients with two different central nervous system diseases, multiple sclerosis and stroke. We have also highlighted the open questions in the field that we believe are important to address to gain a deeper understanding of the mechanisms by which diet can directly or indirectly affect the host via the microbiota. We think this will open up new approaches to the treatment, diagnosis, and monitoring of various diseases.

Lactation-associated macrophages exist in murine mammary tissue and human milk.

Macrophages are involved in immune defense, organogenesis and tissue homeostasis. Macrophages contribute to the different phases of mammary gland remodeling during development, pregnancy and involution postlactation. Less is known about the dynamics of mammary gland macrophages in the lactation stage. Here, we describe a macrophage population present during lactation in mice. By multiparameter flow cytometry and single-cell RNA sequencing, we identified a lactation-induced CD11c+CX3CR1+Dectin-1+ macrophage population (liMac) that was distinct from the two resident F4/80hi and F4/80lo macrophage subsets present pregestationally. LiMacs were predominantly monocyte-derived and expanded by proliferation in situ concomitant with nursing. LiMacs developed independently of IL-34, but required CSF-1 signaling and were partly microbiota-dependent. Locally, they resided adjacent to the basal cells of the alveoli and extravasated into the milk. We found several macrophage subsets in human milk that resembled liMacs. Collectively, these findings reveal the emergence of unique macrophages in the mammary gland and milk during lactation.

Plastics in our ocean as transdisciplinary challenge.

This conference report summarizes the current challenges of researching microplastics pollution in the ocean as debated by international experts and stakeholders at a workshop held in San Sebastián, Spain, 1-2 October 2019. The transdisciplinary, co-learning approach of this report stressed the need to incorporate multiple perspective in solving the problem of microplastics and resulted in three proposed actions: (i) filtering microplastics from waste waters; (ii) mandatory ecolabels on plastic products packages; and (iii) circular economy of packaging plastics.

The Gut-Brain Axis: How Microbiota and Host Inflammasome Influence Brain Physiology and Pathology.

The human microbiota has a fundamental role in host physiology and pathology. Gut microbial alteration, also known as dysbiosis, is a condition associated not only with gastrointestinal disorders but also with diseases affecting other distal organs. Recently it became evident that the intestinal bacteria can affect the central nervous system (CNS) physiology and inflammation. The nervous system and the gastrointestinal tract are communicating through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the vagus nerve, the immune system, and bacterial metabolites and products. During dysbiosis, these pathways are dysregulated and associated with altered permeability of the blood-brain barrier (BBB) and neuroinflammation. However, numerous mechanisms behind the impact of the gut microbiota in neuro-development and -pathogenesis remain poorly understood. There are several immune pathways involved in CNS homeostasis and inflammation. Among those, the inflammasome pathway has been linked to neuroinflammatory conditions such as multiple sclerosis, Alzheimer's and Parkinson's diseases, but also anxiety and depressive-like disorders. The inflammasome complex assembles upon cell activation due to exposure to microbes, danger signals, or stress and lead to the production of pro-inflammatory cytokines (interleukin-1ß and interleukin-18) and to pyroptosis. Evidences suggest that there is a reciprocal influence of microbiota and inflammasome activation in the brain. However, how this influence is precisely working is yet to be discovered. Herein, we discuss the status of the knowledge and the open questions in the field focusing on the function of intestinal microbial metabolites or products on CNS cells during healthy and inflammatory conditions, such as multiple sclerosis, Alzheimer's and Parkinson's diseases, and also neuropsychiatric disorders. In particular, we focus on the innate inflammasome pathway as immune mechanism that can be involved in several of these conditions, upon exposure to certain microbes.

In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes.

The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome's annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, g-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.

Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework.

The 'One Health' framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extraction kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness, while lowest richness was observed in human faeces. Primer pair choice directly influenced the estimation of community changes within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.

Female mating tactics in lekking fallow deer (Dama dama): experience explains inter-individual variability more than costs.

Most studies on ungulate reproduction have focused on the covariates of male reproductive success, while there is much less information on female tactics of mate choice. The aim of this work is to fill this gap and to assess condition-dependent variations in female tactics in a lekking fallow deer (Dama dama) population. In particular, we investigated three indirect selection mechanisms: i) aggregation: when females join an already formed female group; ii) copying: when females copy the mate choice of other females and iii) territory choice: when females select a territory where many copulations had previously occurred. Our results show that female fallow deer, which are less experienced (younger) and/or incur higher travel costs (home range far from the lek), adopt indirect forms of mate selection more often than older females or females residing near the lek, respectively. Compared to adults, younger females remained longer in the lek (almost three times) and in male territories, returning to the lek after copulation. However, despite the time spent at the lek, younger females were not able to select the highest-rank males, and relied on territory choice more often than older females. Farther does visited the lek less frequently (farthest females only once) and arrived on average 5 days later than closer females (which performed up to 7 visits), but they were seen more often within female groups (aggregation). We did not find a different amount of copying in younger or in farther females. Our results contribute to advance our understanding of female behaviours in ungulate leks.

Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy.

Myocarditis can develop into inflammatory cardiomyopathy through chronic stimulation of myosin heavy chain 6-specific T helper (TH)1 and TH17 cells. However, mechanisms governing the cardiotoxicity programming of heart-specific T cells have remained elusive. Using a mouse model of spontaneous autoimmune myocarditis, we show that progression of myocarditis to lethal heart disease depends on cardiac myosin-specific TH17 cells imprinted in the intestine by a commensal Bacteroides species peptide mimic. Both the successful prevention of lethal disease in mice by antibiotic therapy and the significantly elevated Bacteroides-specific CD4+ T cell and B cell responses observed in human myocarditis patients suggest that mimic peptides from commensal bacteria can promote inflammatory cardiomyopathy in genetically susceptible individuals. The ability to restrain cardiotoxic T cells through manipulation of the microbiome thereby transforms inflammatory cardiomyopathy into a targetable disease.

Microbiota-gut brain axis involvement in neuropsychiatric disorders.

Introduction: The microbiota-gut brain (MGB) axis is the bidirectional communication between the intestinal microbiota and the brain. An increasing body of preclinical and clinical evidence has revealed that the gut microbial ecosystem can affect neuropsychiatric health. However, there is still a need of further studies to elucidate the complex gene-environment interactions and the role of the MGB axis in neuropsychiatric diseases, with the aim of identifying biomarkers and new therapeutic targets, to allow early diagnosis and improving treatments. Areas covered: To review the role of MGB axis in neuropsychiatric disorders, prediction and prevention of disease through exploitation, integration, and combination of data from existing gut microbiome/microbiota projects and appropriate other International '-Omics' studies. The authors also evaluated the new technological advances to investigate and modulate, through nutritional and other interventions, the gut microbiota. Expert opinion: The clinical studies have documented an association between alterations in gut microbiota composition and/or function, whereas the preclinical studies support a role for the gut microbiota in impacting behaviors which are of relevance to psychiatry and other central nervous system (CNS) disorders. Targeting MGB axis could be an additional approach for treating CNS disorders and all conditions in which alterations of the gut microbiota are involved.

A harmonized and coordinated assessment of the abundance and composition of seafloor litter in the Adriatic-Ionian macroregion (Mediterranean Sea).

Marine litter is a threat to marine life and an economic burden for coastal communities, but efforts to address the issue are hampered by the lack of data for many countries. We performed the first harmonized assessment of seafloor litter (trawl and visual surveys) in six countries of the Adriatic-Ionian macroregion. Seafloor litter showed an uneven distribution throughout the area, with large differences in litter densities and composition among countries and locations. An emerging problem in the area resulted in short-term & single-use objects that represented the largest fraction of litter. Packaging was the economic sector contributing most to seafloor litter on the continental shelf and upper slope, while in some areas aquaculture (mussel farming) represented a key activity producing marine litter. In coastal areas and bays (e.g. Boka Kotorska bay, Montenegro), seafloor litter was mainly related to construction activities and electronic goods, which are a consequence of fly-tipping/illegal dumping.

Using Precisely Defined in vivo Microbiotas to Understand Microbial Regulation of IgE.

Early life exposure to microbes plays an important role in immune system development. Germ-free mice, or mice colonized with a low-diversity microbiota, exhibit high serum IgE levels. An increase in microbial richness, providing it occurs in a critical developmental window early in life, leads to inhibition of this hygiene-induced IgE. However, whether this inhibition is dependent solely on certain microbial species, or is an additive effect of microbial richness, remains to be determined. Here we report that mice colonized with a combination of bacterial species with specific characteristics is required to inhibit IgE levels. These defined characteristics include the presence in early life, acetate production and immunogenicity reflected by induction of IgA. Suppression of IgE did not correlate with production of the short chain fatty acids propionate and butyrate, or induction of peripherally induced Tregs in mucosal tissues. Thus, inhibition of IgE induction can be mediated by specific microbes and their associated metabolic pathways and immunogenic properties.

Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response.

Although the mammalian microbiota is well contained within the intestine, it profoundly shapes development and metabolism of almost every host organ. We questioned the range and depth of microbial metabolite penetration into the host, and how this is modulated by intestinal immunity. Chemically identical microbial and host metabolites were distinguished by stable isotope tracing from 13C-labeled live non-replicating Escherichia coli, differentiating 12C host isotopes with high-resolution mass spectrometry. Hundreds of endogenous microbial compounds penetrated 23 host tissues and fluids after intestinal exposure: subsequent 12C host metabolome signatures included lipidemia, reduced glycolysis, and inflammation. Penetrant bacterial metabolites from the small intestine were rapidly cleared into the urine, whereas induced antibodies curtailed microbial metabolite exposure by accelerating intestinal bacterial transit into the colon where metabolite transport mechanisms are limiting. Pervasive penetration of microbial molecules can cause extensive host tissue responses: these are limited by immune and non-immune intestinal mucosal adaptations to the microbiota.

Assessment on marine litter ingested by fish in the Adriatic and NE Ionian Sea macro-region (Mediterranean).

This study presents data on the marine litter occurrence in the stomachs of fish species living in different marine habitats for the Adriatic and NE Ionian Sea macro-region. "Macro-litter" was examined in 614 specimens belonging to 11 species, while micro-litter in 230 specimens belonging to 7 species. The study highlights for the first time the presence of litter in the stomachs of the fish species Citharus linguatula. The occurrence of "macro-litter" in the guts of fish was <3% in both the NE Ionian and N Adriatic but reached 26% in the S Adriatic Sea. Micro-litter occurrence was 40 for the NE Ionian and increased to 87% in the N Adriatic (Slovenian Sea). The ingested "macro" and micro-litter differed among the areas. The marine habitat was found to affect the "macro"-litter ingestion but not the micro-litter.

Marine litter on the beaches of the Adriatic and Ionian Seas: An assessment of their abundance, composition and sources.

The abundance, composition and sources of marine litter were determined on beaches located in the seven countries of the Adriatic-Ionian macroregion, namely Albania, Bosnia and Herzegovina, Croatia, Greece, Italy, Montenegro and Slovenia. A total of 70,581 marine litter items were classified and recorded through one-year long surveys carried out in 31 sites. The average litter density of 0.67 items/m2 found within this study is considered to be relatively high. The beaches investigated differed in terms of human-induced pressures; their majority is classified either as semi-urban or semi-rural, while very few beaches could be characterized as urban or remote/natural. The majority of litter items were made of artificial/anthropogenic polymer materials accounting for 91.1% of all litter. Litter from shoreline sources accounted for 33.4% of all litter collected. The amount of litter from sea-based sources ranged in the different countries from 1.54% to 14.84%, with an average of 6.30% at regional level.

Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions.

Several human diseases are thought to evolve due to a combination of host genetic mutations and environmental factors that include alterations in intestinal microbiota composition termed dysbiosis. Although in some cases, host genetics may shape the gut microbiota and enable it to provoke disease, experimentally disentangling cause and consequence in such host-microbe interactions requires strict control over non-genetic confounding factors. Mouse genetic studies previously proposed Nlrp6/ASC inflammasomes as innate immunity regulators of the intestinal ecosystem. In contrast, using littermate-controlled experimental setups, we recently showed that Nlrp6/ASC inflammasomes do not alter the gut microbiota composition. Our analyses indicated that maternal inheritance and long-term separate housing are non-genetic confounders that preclude the use of non-littermate mice when analyzing host genetic effects on intestinal ecology. Here, we summarize and discuss our gut microbiota analyses in inflammasome-deficient mice for illustrating the importance of littermate experimental design in studying host-microbiota interactions.

A Gut Microbial Mimic that Hijacks Diabetogenic Autoreactivity to Suppress Colitis.

The gut microbiota contributes to the development of normal immunity but, when dysregulated, can promote autoimmunity through various non-antigen-specific effects on pathogenic and regulatory lymphocytes. Here, we show that an integrase expressed by several species of the gut microbial genus Bacteroides encodes a low-avidity mimotope of the pancreatic ß cell autoantigen islet-specific glucose-6-phosphatase-catalytic-subunit-related protein (IGRP206-214). Studies in germ-free mice monocolonized with integrase-competent, integrase-deficient, and integrase-transgenic Bacteroides demonstrate that the microbial epitope promotes the recruitment of diabetogenic CD8+ T cells to the gut. There, these effectors suppress colitis by targeting microbial antigen-loaded, antigen-presenting cells in an integrin ß7-, perforin-, and major histocompatibility complex class I-dependent manner. Like their murine counterparts, human peripheral blood T cells also recognize Bacteroides integrase. These data suggest that gut microbial antigen-specific cytotoxic T cells may have therapeutic value in inflammatory bowel disease and unearth molecular mimicry as a novel mechanism by which the gut microbiota can regulate normal immune homeostasis. PAPERCLIP.

Host-microbiota interactions and adaptive immunity.

All mucosal surfaces are colonized with a vast number of microbes, which are essential for stimulating and regulating the immune system. While intrinsic and innate mechanisms exist to promote a strong barrier between the microbiota and the host to ensure compartmentalization, the microbiota is also able to induce robust adaptive immunity. In this review, we discuss the interplay between the microbiota and the adaptive immune system, with a focus on the induction of mucosal and systemic antibody responses and newly defined roles of maternal antibodies. We also highlight recent studies that aim to decipher microbial antigen-specificity of the T-cell compartment.