Peripheral neuronal activation shapes the microbiome and alters gut physiology

The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia. The GI tract also harbors a diverse microbiome, but interactions between the ENS and the microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated neurons in mice to determine effects on intestinal microbial communities and their metabolites as well as on host physiology. The resulting multi-omics datasets support broad roles for discrete peripheral neuronal subtypes in shaping microbiome structure, including modulating bile acid profiles and fungal colonization. Physiologically, activation of either ChAT+ or TH+ neurons increases fecal output, while only ChAT+ activation results in increased colonic contractility and diarrhea-like fluid secretion. These findings suggest that specific subsets of peripherally activated neurons differentially regulate the gut microbiome and GI physiology in mice without involvement of signals from the brain.

True, justified, belief? Partisanship weakens the positive effect of news media literacy on fake news detection

To investigate how people assess whether politically consistent news is real or fake, two studies (N = 1,008; N = 1,397) with adult American participants conducted in 2020 and 2022 utilized a within-subjects experimental design to investigate perceptions of news accuracy. When a mock Facebook post with either fake (Study 1) or real (Study 2) news content was attributed to an alternative (vs. a mainstream) news outlet, it was, on average, perceived to be less accurate. Those with beliefs reflecting News Media Literacy demonstrated greater sensitivity to the outlet's status. This relationship was itself contingent on the strength of the participant's partisan identity. Strong partisans high in News Media Literacy defended the accuracy of politically consistent content, even while recognizing that an outlet was unfamiliar. These results highlight the fundamental importance of looking at the interaction between user-traits and features of social media news posts when examining learning from political news on social media.

Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome

BACKGROUND

The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD).

OBJECTIVES

The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression.

METHODS

Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features.

RESULTS

We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling.

CONCLUSIONS

A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Microbiota regulate social behaviour via stress response neurons in the brain

Social interactions among animals mediate essential behaviours, including mating, nurturing, and defence^1,2. The gut microbiota contribute to social activity in mice^3,4, but the gut-brain connections that regulate this complex behaviour and its underlying neural basis are unclear^5,6. Here we show that the microbiome modulates neuronal activity in specific brain regions of male mice to regulate canonical stress responses and social behaviours. Social deviation in germ-free and antibiotic-treated mice is associated with elevated levels of the stress hormone corticosterone, which is primarily produced by activation of the hypothalamus-pituitary-adrenal (HPA) axis. Adrenalectomy, antagonism of glucocorticoid receptors, or pharmacological inhibition of corticosterone synthesis effectively corrects social deficits following microbiome depletion. Genetic ablation of glucocorticoid receptors in specific brain regions or chemogenetic inactivation of neurons in the paraventricular nucleus of the hypothalamus that produce corticotrophin-releasing hormone (CRH) reverse social impairments in antibiotic-treated mice. Conversely, specific activation of CRH-expressing neurons in the paraventricular nucleus induces social deficits in mice with a normal microbiome. Via microbiome profiling and in vivo selection, we identify a bacterial species, Enterococcus faecalis, that promotes social activity and reduces corticosterone levels in mice following social stress. These studies suggest that specific gut bacteria can restrain the activation of the HPA axis, and show that the microbiome can affect social behaviours through discrete neuronal circuits that mediate stress responses in the brain.

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD or TD controls into germ-free mice and reveal that colonization with ASD microbiota is sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and modulates neuronal excitability in the brain. We propose that the gut microbiota regulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.

Liposarcoma in clownfish, Amphiprion ocellaris Cuvier, produced in indoor aquaculture

Clownfish, Amphiprion ocellaris Cuvier, produced and grown in an experimental indoor aquaculture facility, presented with lipomatous tumours. A total of 14 affected fish were examined. Based on the total number of fish at the aquaculture facility at the time of outbreak of this pathology, the scope of the incident is estimated to be 1 of 300 fish. The tumours were characterized by the presence of mature adipocytes of variable sizes, lipoblasts and by an invasive behaviour, which affected internal organs, muscle, central nervous system and, in one case, an eye. Detailed macroscopic and histopathological features are presented. The suggested diagnosis is that of a well-differentiated liposarcoma, a diagnosis so far never applied to fish. The limited outbreak of the neoplasm lasted a few months in 2011 and did not recur. Possible factors leading to this phenomenon, notably the metastasis, are discussed.

Controlled infection of Poecilia reticulata Peters (guppy) with Tetrahymena by immersion and intraperitoneal injection

Tetrahymena is a protozoan parasite, which infects guppy, Poecilia reticulata Peters, and causes substantial economical losses in commercial farms worldwide. Studies of guppy infected by Tetrahymena require standardized infection protocols. The LD50 for Tetrahymena infection of guppies by intraperitoneal (IP) injection was calibrated, and the level obtained was 946 parasites per fish. Guppy infection with Tetrahymena by immersion, imitating the natural route of infection via the integument, was studied under normal or stress conditions. Exposure to cold and netting (CNI) and to cold only (CI) followed by immersion exposure to 10 000 Tetrahymena per mL resulted in 22.5% and 19.2% mortality, respectively, as compared to 14.2% and 10% in groups that were netted only (NI) or non-stressed (I). Histopathology revealed that immersion infection resulted in a systemic infection. Lysozyme levels, measured 3 weeks after infection, were significantly higher in the CNI group (288 μg per mg protein) compared with CI-, NI- and I-treated groups (94.5, 64 and 62.3 μg mg(-1), respectively). There was no evident parasite immobilization activity in body homogenates, suggesting no development of acquired immunity. Re-infection by IP injection revealed no increase in protection in any of the treatment groups, mortality range of 56.3-75%, higher than in the non-exposed control (40.6% mortality).

Specialized metabolites from the microbiome in health and disease

The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects on the host. We propose that the effects of specialized metabolites may explain present knowledge gaps in linking the gut microbiota to biological host mechanisms during initial colonization, and in health and disease.

Enhanced Partial Expansion A*

When solving instances of problem domains that feature a large branching factor, A* may generate a large number of nodes whose cost is greater than the cost of the optimal solution. We designate such nodes as surplus. Generating surplus nodes and adding them to the OPEN list may dominate both time and memory of the search. A recently introduced variant of A* called Partial Expansion A* (PEA*) deals with the memory aspect of this problem. When expanding a node n, PEA* generates all of its children and puts into OPEN only the children with f = f (n). n is re-inserted in the OPEN list with the f -cost of the best discarded child. This guarantees that surplus nodes are not inserted into OPEN. In this paper, we present a novel variant of A* called Enhanced Partial Expansion A* (EPEA*) that advances the idea of PEA* to address the time aspect. Given a priori domain- and heuristic- specific knowledge, EPEA* generates only the nodes with f = f(n). Although EPEA* is not always applicable or practical, we study several variants of EPEA*, which make it applicable to a large number of domains and heuristics. In particular, the ideas of EPEA* are applicable to IDA* and to the domains where pattern databases are traditionally used. Experimental studies show significant improvements in run-time and memory performance for several standard benchmark applications. We provide several theoretical studies to facilitate an understanding of the new algorithm.

Symbiotic bacteria are responsible for diet-induced mating preference in Drosophila melanogaster, providing support for the hologenome concept of evolution

Diet-induced mating preference in Drosophila melanogaster results from amplification of the commensal bacterium Lactobacillus plantarum, providing a new role for gut microbiota and support for the hologenome concept of evolution. When the flies were treated with antibiotics prior to changing their diet, mating preference did not occur. These data also indicate that other potentially beneficial bacteria could be irreversibly lost by antibiotic treatment and that their replacement could provide a health benefit. We suggest that D. melanogaster can be a useful model organism to study the activities of gut microbiota and their interaction with the immune system.

Bacteria-induced sexual isolation in Drosophila

Commensal bacteria can induce sexual isolation between populations of Drosophila. This phenomenon has implications for speciation, and raises questions about its behavioral and developmental mechanisms, which are not yet known. In this Extra View, we discuss related work by others, bearing directly on these issues, and we speculate about how bacteria might influence fly behavior. There are many reports of interaction between Drosophila and their microbiota that significantly impacts mating preferences. Sexual isolation can be enhanced or reduced by altering the culture media, or the microbiota inhabiting those media. More dramatically, the endoparasite Wolbachia has induced strong mate preferences in some instances. While a sudden, ecologically induced shift in mating preferences falls far short of the changes required for speciation, it might be a first step in that direction. We hypothesize that bacteria-induced sexual isolation is caused by chemosensory cues. In our experiments, bacteria altered the profile of cuticular hydrocarbons, which function as sex pheromones. Commensal bacteria may act directly on these hydrocarbons, or they may affect their synthesis. Alternatively, bacterial metabolites might perfume the flies in ways that affect mate choice. In that event, habituation or conditioning likely plays a role.

The phage-driven microbial loop in petroleum bioremediation

During the drilling process and transport of crude oil, water mixes with the petroleum. At oil terminals, the water settles to the bottom of storage tanks. This drainage water is contaminated with emulsified oil and water‐soluble hydrocarbons and must be treated before it can be released into the environment. In this study, we tested the efficiency of a continuous flow, two‐stage bioreactor for treating drainage water from an Israeli oil terminal. The bioreactor removed all of the ammonia, 93% of the sulfide and converted 90% of the total organic carbon (TOC) into carbon dioxide. SYBR Gold staining indicated that reactor 1 contained 1.7 × 10⁸ bacteria and 3.7 × 10⁸ phages per millilitre, and reactor 2 contained 1.3 × 10⁸ bacteria and 1.7 × 10⁹ phages per millilitre. The unexpectedly high mineralization of TOC and high concentration of phage in reactor 2 support the concept of a phage‐driven microbial loop in the bioremediation of the drainage water. In general, application of this concept in bioremediation of contaminated water has the potential to increase the efficiency of processes.

The evolution of animals and plants via symbiosis with microorganisms

Animals and plants evolved from prokaryotes and have remained in close association with them. We suggest that early eukaryotic cells, formed by the fusion of two or more prokaryotes, already contained prokaryotic genetic information for aggregation and the formation of multicellular structures. The hologenome theory of evolution posits that a unit of selection in evolution is the holobiont (host plus symbionts). The hologenome is defined as the genetic information of the host and its microbiota, which function in consortium. Genetic variation of the holobiont, the raw material for evolution, can arise from changes in either the host or the symbiotic microbiota genomes. Changes in the hologenome can occur by two processes that are specific to holobionts: microbial amplification and acquisition of novel strains from the environment. Recent data from culture-independent studies provides considerable support of the hologenome theory: (i) all animals and plants contain abundant and diverse microbiota, (ii) the symbiotic microbiota affects the fitness of their host and (iii) symbiotic microorganisms are transmitted from parent to offspring. Consideration of the dynamic aspects of symbioses of hosts with their diverse microbiota leads to the conclusion that holobionts can evolve not only via Darwinian but also by adaptive Lamarckian principles.

Healthy corals maintain Vibrio in the VBNC state

Vibrio species play an important role in the health and disease of corals. To gain a better understanding of the interactions between Vibrio and coral holobionts we examined the growth of Vibrio in the mucus of the coral Oculina patagonica while the mucus was attached and detached from the coral. Fresh mucus contained ca. 10(2) Vibrio cfu ml(-1) , representing c. 1% of the total viable count. Incubation of detached mucus resulted in a 50 000-fold increase in Vibrio cfu from 1 to 4 h, corresponding to 60% of the total viable counts. This large increase in Vibrio would require an unreasonable doubling time of 11 min. Furthermore, the total microscopic bacterial count increased only 17-fold during the 1-4 h incubation period. These data led to the conclusion that Vibrio species in the mucus were largely in the VBNC state when attached to the coral and 'resuscitated' when the mucus was detached from the coral. We suggest that the coral signal for maintaining Vibrio in the VBNC state is diffusible and unstable. Maintenance of Vibrio in the VBNC state did not require photosynthetic products of the coral holobiont. Vibrio species in the VBNC state may contribute to the health of corals by preventing infections by pathogens.

The Acheulean massive scrapers of Gesher Benot Ya'aqov-a product of the biface chaîne opératoire

The presence of large scrapers has been reported from Acheulean sites worldwide but they are rarely described in detail. At Gesher Benot Ya'aqov (GBY), a similar group of artifacts, named here "massive scrapers," was identified as a significant component of the lithic assemblage. In this paper, we define and describe this Acheulean tool type and discuss its size, morphology, and technology. We demonstrate that at GBY these tools were shaped on flakes that were side-products of the reduction sequence to produce bifaces (handaxes and cleavers). We hypothesize that these blanks were rejected as potential bifaces during the knapping sequence but considered suitable for the retouching of massive scrapers, and were set aside for future work. We support our view with data from archaeological finds younger than those of GBY, as well as with evidence from controlled experimental knapping and ethnoarchaeological observations. We then discuss the contribution of this elaborate knapping strategy to our understanding of Lower Paleolithic hominin behavior, particularly in the domains of multifaceted planning and foresight.

Thalassomonas loyana sp. nov., a causative agent of the white plague-like disease of corals on the Eilat coral reef

The taxonomic position of the coral pathogen strain CBMAI 722T was determined on the basis of molecular and phenotypic data. We clearly show that the novel isolate CBMAI 722 T is a member of the family Colwelliaceae, with Thalassomonas ganghwensis as the nearest neighbour (95 % 16S rRNA gene sequence similarity). CBMAI 722T can be differentiated from its nearest neighbour on the basis of phenotypic and chemotaxonomic features, including the utilization of cellobiose and L-arginine, the production of alginase and amylase, but not oxidase, and the presence of the fatty acids 12:0 3-OH and 14:0, but not 10:0 or 15:0. The DNA G+C content of CBMAI 722T is 39.3 mol%. We conclude that this strain represents a novel species for which we propose the name Thalassomonas loyana sp. nov., with the type strain CBMAI 722T (=LMG 22536T). This is the first report of the involvement of a member of the family Colwelliaceae in coral white plague-like disease.

Stop codons affect 5' splice site selection by surveillance of splicing

Pre-mRNA splicing involves recognition of a consensus sequence at the 5' splice site (SS). However, only some of the many potential sites that conform to the consensus are true ones, whereas the majority remain silent and are not normally used for splicing. We noticed that in most cases the utilization of such a latent intronic 5' SS for splicing would introduce an in-frame stop codon into the resultant mRNA. This finding suggested a link between SS selection and maintenance of an ORF within the mRNA. Here we tested this idea by analyzing the splicing of pre-mRNAs in which in-frame stop codons upstream of a latent 5' SS were mutated. We found that splicing with the latent site is indeed activated by such mutations. Our findings predict the existence of a checking mechanism, as a component of the nuclear pre-mRNA splicing machine, to ensure the maintenance of an ORF. This notion is highly important for accurate gene expression, as perturbations that would lead to splicing at these latent sites are expected to introduce in-frame stop codons into the majority of mRNAs.

Cellular and viral splicing factors can modify the splicing pattern of CFTR transcripts carrying splicing mutations

Variable levels of aberrantly spliced cystic fibrosis transmembrane conductance regulator (CFTR ) transcripts were suggested to correlate with variable cystic fibrosis (CF) severity. We studied the effect of the cellular splicing factors, hnRNP A1 and ASF/SF2, and their adenoviral analogues, E4-ORF6 and E4-ORF3, that promote exon skipping and/or exon inclusion, on the splicing pattern of the CFTR mutation 3849+10kb C-->T and the 5T allele. These mutations can lead to cryptic exon inclusion and exon skipping, respectively. Overexpression of the cellular factors promoted exon skipping of pre-mRNA transcribed from minigenes carrying the mutation (p5T or p3849M). This led to a substantial decrease in the level of correctly spliced mRNA transcribed from p5T and generated correctly spliced mRNA transcribed from p3849M that was not found without overexpression of the factors. The viral factor, E4-ORF3, promoted exon inclusion and led to a substantial increase of the correctly spliced mRNA transcribed from the p5T. The factor, E4-ORF6, activated exon skipping and generated correctly spliced mRNA transcribed from p3849M. Thus, overexpression of alternative splicing factors can modulate the splicing pattern of CFTR alleles carrying splicing mutations. These results are important for understanding the mechanism underlying phenotypic variability in CF and other genetic diseases.

Efficient homologous recombination of Ty1 element cDNA when integration is blocked

Integration of the yeast retrotransposon Ty1 into the genome requires the self-encoded integrase (IN) protein and specific terminal nucleotides present on full-length Ty1 cDNA. Ty1 mutants with defects in IN, the conserved termini of Ty1 cDNA, or priming plus-strand DNA synthesis, however, were still able to efficiently insert into the genome when the elements were expressed from the GAL1 promoter present on a multicopy plasmid. As with normal transposition, formation of the exceptional insertions required an RNA intermediate, Ty1 reverse transcriptase, and Ty1 protease. In contrast to Ty1 transposition, at least 70% of the chromosomal insertions consisted of complex multimeric Ty1 elements. Ty1 cDNA was transferred to the inducing plasmid as well as to the genome, and transfer required the recombination and repair gene RAD52. Furthermore, multimeric insertions occurred without altering the levels of total Ty1 RNA, virus-like particle-associated RNA or cDNA, Ty1 capsid proteins, or IN. These results suggest that Ty1 cDNA is utilized much more efficiently for homologous recombination when IN-mediated integration is blocked.

RAD6 gene product of Saccharomyces cerevisiae requires a putative ubiquitin protein ligase (E3) for the ubiquitination of certain proteins

The RAD6 (UBC2) gene of Saccharomyces cerevisiae which is involved in DNA repair, induced mutagenesis, and sporulation, encodes a ubiquitin-conjugating enzyme (E2). Since the RAD6 gene product can transfer ubiquitin directly to histones in vitro without the participation of a ubiquitin protein ligase (E3), it has been suggested that in vivo it also acts by the unassisted conjugation of ubiquitin to histones or to other target proteins. Here we show that the RAD6 protein can ligate ubiquitin in vitro to a hitherto unknown set of exogenous target proteins (alpha-, beta-, and kappa-casein and beta-lactoglobulin) when supplemented by a putative ubiquitin protein ligase (E3-R) from S. cerevisiae. RAD6 supplemented with E3-R ligates 1 or, sometimes, 2 ubiquitin molecules to the target protein molecule. UBC3 (CDC34) protein in the presence of E3-R has barely detectable activity on the non-histone substrates. Other ubiquitin-conjugating enzymes tested (products of the UBC1 and UBC4 genes) do not cooperate with E3-R in conjugating ubiquitin to the same substrates. Thus, E3-R apparently interacts selectively with RAD6 protein. These findings suggest that some of the in vivo activities of the RAD6 gene may involve E3-R.

Centromeric regions control autonomous segregation tendencies in single-division meiosis of Saccharomyces cerevisiae

We have previously shown that yeast cdc5 or cdc14 homozygotes can be led through a single-division meiosis in which some of the chromosomes segregate reductionally whereas others, within the same cell, segregate equationally. Chromosomes XI tend to segregate reductionally, whereas chromosomes IV tend to segregate equationally. In this report we present experiments with cdc5 homozygous strains, in which the centromeres of one or both chromosomes XI was replaced by the centromeric region from chromosome IV. Analysis of the products of single-division meioses in these strains demonstrates that the choice between reductional or equational segregation is directed by sequences in the vicinity of the centromeres. Although the choice is made separately for each individual chromosome, the analysis also reveals the existence of a system responsible for coordinated segregation of the two chromosomes of a given pair.

Mixed segregation of chromosomes during single-division meiosis of Saccharomyces cerevisiae

Normal meiosis consists of two consecutive cell divisions in which all the chromosomes behave in a concerted manner. Yeast cells homozygous for the mutation cdc5, however, may be directed through a single meiotic division of a novel type. Dyad analysis of a cdc5/cdc5 strain with centromere-linked markers on four different chromosomes has shown that, in these meioses, some chromosomes within a given cell segregate reductionally whereas others segregate equationally. The choice between the two types of segregation in these meioses is made individually by each chromosome pair. Different chromosome pairs exhibit different segregation tendencies. Similar results were obtained for cells homozygous for cdc14.

Efficacy of oral mexiletine therapy at a 12-h dosage interval

The antiarrhythmic effectiveness and safety of 12-h oral administration of mexiletine were evaluated in adult outpatients with a baseline hourly rate of PVCs of 30 or higher who had initially shown at least a 50 percent reduction of this rate when treated with mexiletine at an 8-h dosage interval. Doses were titrated on the basis of 24-h Holter monitoring for both 8- and 12-h intervals. Seventeen of 26 patients showed PVC reductions after 8-h treatment. Fifteen of these 17 patients reached the goal reduction of greater than or equal to 50 percent in the hourly PCV rate with 12-h dosing. Hour-by-hour analysis disclosed a consistent degree of PVC suppression throughout both 8- and 12-h dose intervals. No increase in the incidence of adverse effects was associated with conversion to the 12-h regimen.