Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina

Lichens are composite, symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the world's most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here, we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes across the sampled thalli, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing the occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Metatranscriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared with axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signaling, transcriptional regulation, and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.

Gut microbiota: A new window for the prevention and treatment of neuropsychiatric disease

Under normal physiological conditions, gut microbiota and host mutually coexist. They play key roles in maintaining intestinal barrier integrity, absorption, and metabolism, as well as promoting the development of the central nervous system (CNS) and emotional regulation. The dysregulation of gut microbiota homeostasis has attracted significant research interest, specifically in its impact on neurological and psychiatric disorders. Recent studies have highlighted the important role of the gut- brain axis in conditions including Alzheimer's Disease (AD), Parkinson's Disease (PD), and depression. This review aims to elucidate the regulatory mechanisms by which gut microbiota affect the progression of CNS disorders via the gut-brain axis. Additionally, we discuss the current research landscape, identify gaps, and propose future directions for microbial interventions against these diseases. Finally, we provide a theoretical reference for clinical treatment strategies and drug development for AD, PD, and depression.

From eggs to guts: Symbiotic association of Sodalis nezarae sp. nov. with the Southern green shield bug Nezara viridula

Phytophagous insects engage in symbiotic relationships with bacteria that contribute to digestion, nutrient supplementation, and development of the host. The analysis of shield bug microbiomes has been mainly focused on the gut intestinal tract predominantly colonized by Pantoea symbionts and other microbial community members in the gut or other organs have hardly been investigated. In this study, we reveal that the Southern green shield bug Nezara viridula harbours a Sodalis symbiont in several organs, with a notable prevalence in salivary glands, and anterior regions of the midgut. Removing external egg microbiota via sterilization profoundly impacted insect viability but did not disrupt the vertical transmission of Sodalis and Pantoea symbionts. Based on the dominance of Sodalis in testes, we deduce that N. viridula males could be involved in symbiont vertical transmission. Genomic analyses comparing Sodalis species revealed that Sodalis sp. Nvir shares characteristics with both free-living and obligate insect-associated Sodalis spp. Sodalis sp. Nvir also displays genome instability typical of endosymbiont lineages, which suggests ongoing speciation to an obligate endosymbiont. Together, our study reveals that shield bugs harbour unrecognized symbionts that might be paternally transmitted.

Genomes of the Bacterial Endosymbionts of Carrot Psyllid Trioza apicalis Suggest Complementary Biosynthetic Capabilities

Carrot psyllid Trioza apicalis is a serious pest of cultivated carrot and also a vector of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso). To find out whether T. apicalis harbours other species of bacteria that might affect the Lso infection rate, the bacterial communities and metagenome in T. apicalis were studied. Lso haplotype C was detected in a third of the psyllids sampled, at different relative amounts. Surprisingly, T. apicalis was found to harbour only one secondary endosymbiont, a previously unknown species of gamma proteobacterium endosymbiont (Gpe), beside the primary endosymbiont 'Candidatus Carsonella ruddii' (CCr). The relative abundancies of these two endosymbionts were approximately equal. The genomes of CCr, Gpe and Lso were assembled from a T. apicalis metagenome sample. Based on the 16S rRNA gene, the closest relative of Gpe of T. apicalis could be a secondary endosymbiont of Trioza magnoliae. The 253.171 kb Gpe genome contains all the tRNA and rRNA genes and most of the protein-coding genes required for DNA replication, transcription and translation, but it lacks most of the genes for amino acid biosynthesis. Gpe has no genes encoding cell wall peptidoglycan synthesis, suggesting it has no cell wall, and could thus live as an intracellular endosymbiont. Like the CCr of other psyllids, CCr of T. apicalis retains a broad amino acid biosynthetic capacity, whilst lacking many genes required for DNA replication and repair and for transcription and translation. These findings suggest that these two endosymbionts of T. apicalis are complementary in their biosynthetic capabilities.

Unveiling the Mechanisms of Pain in Endometriosis: Comprehensive Analysis of Inflammatory Sensitization and Therapeutic Potential

Endometriosis is a complicated, estrogen-dependent gynecological condition with a high morbidity rate. Pain, as the most common clinical symptom of endometriosis, severely affects women's physical and mental health and exacerbates socioeconomic burden. However, the specific mechanisms behind the occurrence of endometriosis-related pain remain unclear. It is currently believed that the occurrence of endometriosis pain is related to various factors, such as immune abnormalities, endocrine disorders, the brain-gut axis, angiogenesis, and mechanical stimulation. These factors induce systemic chronic inflammation, which stimulates the nerves and subsequently alters neural plasticity, leading to nociceptive sensitization and thereby causing chronic pain. In this paper, we compile and review the articles published on the study of nociceptive sensitization and endometriosis pain mechanisms. Starting from the factors influencing the chronic pain associated with endometriosis, we explain the relationship between these factors and chronic inflammation and further elaborate on the potential mechanisms by which chronic inflammation induces nociceptive sensitization. We aim to reveal the possible mechanisms of endometriosis pain, as well as nociceptive sensitization, and offer potential new targets for the treatment of endometriosis pain.

A general and biomedical perspective of viral quasispecies

Viral quasispecies refers to the complex and dynamic mutant distributions (also termed mutant spectra, clouds, or swarms) that arise as a result of high error rates during RNA genome replication. The mutant spectrum of individual RNA virus populations is modified by continuous generation of variant genomes, competition and interactions among them, environmental influences, bottleneck events, and bloc transmission of viral particles. Quasispecies dynamics provides a new perspective on how viruses adapt, evolve, and cause disease, and sheds light on strategies to combat them. Molecular flexibility, together with ample opportunity of mutant cloud traffic in our global world, are key ingredients of viral disease emergences, as exemplified by the recent COVID-19 pandemic. In the present article, we present a brief overview of the molecular basis of mutant swarm formation and dynamics, and how the latter relates to viral disease and epidemic spread. We outline future challenges derived of the highly diverse cellular world in which viruses are necessarily installed.

Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.

IMPORTANCE

Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.

From genes to nanotubes: exploring the UV-resistome in the Andean extremophile Exiguobacterium sp. S17

Exiguobacterium sp. S17, a polyextremophile isolated from a High-Altitude Andean Lake, exhibits a multi-resistance profile against toxic arsenic concentrations, high UV radiation, and elevated salinity. Here, we characterize the mechanisms underlying the UV resistance of Exiguobacterium sp. S17 (UV-resistome) through comparative genomics within the Exiguobacterium genus and describe morphological and ultrastructural changes using Scanning (SEM) and Transmission (TEM) Electron Microscopy.UV-resistome in Exiguobacterium species ranges from 112 to 132 genes. While we anticipated Exiguobacterium sp. S17 to lead the non-HAAL UV-resistome, it ranked eleventh with 113 genes. This larger UV-resistome in Exiguobacterium spp. aligns with their known adaptation to extreme environments. With SEM/TEM analyses we observed the formation of nanotubes (NTs), a novel finding in Exiguobacterium spp., which increased with higher UV-B doses. These NTs, confirmed to be membranous structures through sensitivity studies and imaging, suggest a role in cellular communication and environmental sensing. Genomic evidence supports the presence of essential NT biogenesis genes in Exiguobacterium sp. S17, further elucidating its adaptive capabilities.Our study highlights the complex interplay of genetic and phenotypic adaptations enabling Exiguobacterium sp. S17 to thrive in extreme UV environments. The novel discovery of NTs under UV stress presents a new avenue for understanding bacterial survival strategies in harsh conditions.

Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization

Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.

Reproductive tract microbiome dysbiosis associated with gynecological diseases

Female health and the microbiota of the reproductive tract are closely associated. The research scope on reproductive tract microbiota extends from the vaginal to the upper reproductive tract and from infectious diseases to various benign and malignant gynecological and obstetrical diseases. The primary focus of this paper was to evaluate the most recent findings about the role of reproductive tract microbiota in gynecological diseases, including endometrial polyps, uterine fibroids, endometriosis, adenomyosis, endometrial hyperplasia, and endometrial carcinoma. Different stages of gynecological diseases have diverse microbiota in the female reproductive tract, and some specific bacteria may help the disease progress. For example, Fusobacterium may exacerbate endometriosis, while treatments that target microbiota, such as antibiotics, probiotics, and flora transplantation, showed some efficacy in the experiment. These findings indicate the wonderful prospect of this field. Additionally, we have discussed how microbiome research can improve our understanding of the interactions between reproductive tract microorganisms and hosts, aid in the screening and diagnosis of gynecological diseases, and direct the development of preventive and therapeutic strategies aimed at maintaining and restoring a healthy reproductive tract microbiota when combined with other technologies like transcriptome and proteome, in vitro cultured cells, and animal models.

Sexual dimorphism in immunity and longevity among the oldest old

Human longevity is a sex-biased process in which sex chromosomes and sex-specific immunity may play a crucial role in the health and lifespan disparities between men and women. Generally, women have a higher life expectancy than men, exhibiting lower infection rates for a broad range of pathogens, which results in a higher prevalence of female centenarians compared to males. Investigation of the immunological changes that occur during the process of healthy aging, while taking into account the differences between sexes, can significantly enhance our understanding of the mechanisms that underlie longevity. In this review, we aim to summarize the current knowledge on sexual dimorphism in the human immune system and gut microbiome during aging, with a particular focus on centenarians, based exclusively on human data.

Maternal obesity, age and infant sex influence the profiles of amino acids, energetic metabolites, sugars, and fatty acids in human milk

PURPOSE

This study aimed to evaluate whether maternal nutritional status, maternal age, mode of delivery, and the infant's sex influence the profiles of amino acids, energetic metabolites, sugars, and fatty acids and as well as the metabolic pathways in mature human milk human milk (HM).

METHODS

This was a cross-sectional, prospective, and observational study. HM samples from normal weight (NW, n = 60), overweight (OW, n = 35), and obese (OB, n = 14) women were analyzed using a non-targeted GC-MS method to identify the metabolome. Data obtained were analyzed with Metaboanalyst software (v. 5.0) and SPSS (v.25.0).

RESULTS

OB women HM contains a higher proportion of amino acids such as leucine, lysine, tyrosine, and aspartic acid, energy metabolites such as lactic and succinic acid, and sugars and derivatives such as fucose, rhamnose, and gluconic acid (p < 0.05) compared with normal weight women HM. HM from women > 25 years of age contains a lower proportion of lauric acid and a higher proportion of leucine and tyrosine (p < 0.05) than ≤ 25 years women HM. Also, HM intended for female infants has a higher leucine and gluconic acid content. The main altered metabolic pathways in OB women HM correspond to amino acids and energetic metabolism.

CONCLUSION

OB women HM provides more amino acids, energetic molecules, and sugars. Increased maternal weight, BMI, and body fat mass predispose to more leucine and aspartic acid in HM. Maternal age influences lauric acid, leucin, and tyrosine levels, while the infant's sex influences leucine and gluconic acid levels in HM. The impact of obese women's HM metabolome on the offspring's physiology needs to be explored.

TRIAL REGISTRATION

R-2021-785-096.

Identification of distinct stool metabolites in women with endometriosis for non-invasive diagnosis and potential for microbiota-based therapies

BACKGROUND

Endometriosis, a poorly studied gynecological condition, is characterized by the presence of ectopic endometrial lesions resulting in pelvic pain, inflammation, and infertility. These associated symptoms contribute to a significant burden, often exacerbated by delayed diagnosis. Current diagnostic methods involve invasive procedures, and existing treatments provide no cure.

METHODS

Microbiome-metabolome signatures in stool samples from individuals with and without endometriosis were determined using unbiased metabolomics and 16S bacteria sequencing. Functional studies for selected microbiota-derived metabolites were conducted in vitro using patient-derived cells and in vivo by employing murine and human xenograft pre-clinical disease models.

FINDINGS

We discovered a unique bacteria-derived metabolite signature intricately linked to endometriosis. The altered fecal metabolite profile exhibits a strong correlation with that observed in inflammatory bowel disease (IBD), revealing intriguing connections between these two conditions. Notably, we validated 4-hydroxyindole, a gut-bacteria-derived metabolite that is lower in stool samples of endometriosis. Extensive in vivo studies found that 4-hydroxyindole suppressed the initiation and progression of endometriosis-associated inflammation and hyperalgesia in heterologous mouse and in pre-clinical models of the disease.

CONCLUSIONS

Our findings are the first to provide a distinct stool metabolite signature in women with endometriosis, which could serve as stool-based non-invasive diagnostics. Further, the gut-microbiota-derived 4-hydroxyindole poses as a therapeutic candidate for ameliorating endometriosis.

FUNDING

This work was funded by the NIH/NICHD grants (R01HD102680, R01HD104813) and a Research Scholar Grant from the American Cancer Society to R.K.

Reproduction in yellow drum (Nibea albiflora): insights from endocrine regulation and intestinal microbiota changes during reproductive season

The yellow drum (Nibea albiflora), a pivotal species within the Sciaenidae family, is economically important in the mariculture along the coastal regions of China. A comprehensive understanding gonadal maturation and spawning processes is crucial for seed production in the artificial propagation of yellow drum. This study investigates serum hormonal fluctuations, gonadal histological features, sex hormone receptor gene expression, and intestinal microbiota composition in both male and female yellow drum during the reproductive season. Twenty individuals were sampled from reproductive stages IV, V, and VI, respectively. During the spawning season, no significant differences were observed in the levels of PROG, E2, and 11-KT across different stages, in both males and females, with no significant sex-based differences. Subsequent analysis indicated a significant upregulation of fshr, lhcgr, and esr expression in the ovary during spawning stages. In contrast, within the testis, the expression levels of fshr, ar, and esr remained relatively constant across different stages, whereas lhcgr expression was markedly higher during the spawning stages compared with prespawning and post-spawning stages. Analysis of intestinal microbiota revealed a predominance of Bacteroidota, Firmicutes, and Proteobacteria, with no significant sex differences. At the class level, the abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacilli exhibited significant fluctuations during the spawning and post-spawning stages in both sexes. At the genus level, g_Muribaculaceae and g_Bacteroides were abundant during spawning stages in both sexes. A Mantel test showed significant positive correlations between PROG levels and the abundances of g_Bacteroides in males. In females, PROG levels were positively correlated with the abundance of g_Prevotella. These findings enhance our understanding of the interplay between reproductive biology and the biological functions of intestinal microbiota in yellow drum broodstock during the reproductive season, thereby laying a foundation for the development of artificial propagation technology in this species.

Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference

Viral phylodynamics focuses on using sequence data to make inferences about the population dynamics of viral diseases. These inferences commonly include estimation of growth rates, reproduction numbers and times of most recent common ancestor. With few exceptions, existing phylodynamic inference approaches assume that all observed and ancestral viral genetic variation is fitness-neutral. This assumption is commonly violated, with a large body of analyses indicating that fitness varies substantially among genotypes circulating in viral populations. Here, we focus on fitness variation arising from deleterious mutations, asking whether incomplete purifying selection of deleterious mutations has the potential to bias phylodynamic inference. We use simulations of an exponentially growing population to explore how incomplete purifying selection distorts tree shape and shifts the distribution of mutations over trees. We find that incomplete purifying selection strongly shapes the distribution of mutations while only weakly impacting tree shape. Despite incomplete purifying selection shifting the distribution of deleterious mutations, we find little discernible bias in estimates of viral growth rates and times of the most recent common ancestor. Our results reassuringly indicate that existing phylodynamic inference approaches that assume neutrality may nevertheless yield accurate epidemiological estimates in the face of incomplete purifying selection. More work is needed to assess the robustness of these findings to alternative epidemiological parametrizations.This article is part of the theme issue ''"A mathematical theory of evolution": phylogenetic models dating back 100 years'.

Molecular Evolution of the Fusion (F) Genes in Human Parainfluenza Virus Type 2

Human parainfluenza virus type 2 (HPIV2) is a clinically significant respiratory pathogen, which highlights the necessity of studies on its molecular evolution. This study investigated the evolutionary dynamics, phylodynamics, and structural characteristics of the HPIV2 fusion (F) gene using a comprehensive dataset spanning multiple decades and geographic regions. Phylogenetic analyses revealed two distinct clusters of HPIV2 F gene sequences, which were estimated to have diverged from a common ancestor approximately a century ago. Cluster 1 demonstrated a higher evolutionary rate and genetic diversity compared to the more stable cluster 2. Bayesian Skyline Plot analyses indicated a significant increase in the effective population size of the F gene between 2005 and 2015; potentially linked to enhanced diagnostic and surveillance capabilities. Structural modeling identified conserved conformational epitopes predominantly in the apex and stalk regions of the F protein. These findings underscore the evolutionary constraints and antigenic landscape of the HPIV2 F protein.

Quinoa Ethanol Extract Ameliorates Cognitive Impairments Induced by Hypoxia in Mice: Insights into Antioxidant Defense and Gut Microbiome Modulation

Quinoa, rich in pharmacologically active ingredients, possesses the potential benefit in preventing cognitive impairments induced by hypoxia. In this study, the efficacy of quinoa ethanol extracts (QEE) consumption (200 and 500 mg/kg/d, respectively) against hypobaric hypoxia (HH)-induced cognitive deficits in mice was investigated. QEE significantly ameliorated hypoxic stress induced by HH, as evidenced by improvements in baseline indices and reductions in hypoxia-inducible factor 1α levels. Furthermore, QEE enhanced antioxidant defense mechanisms, alleviated neuroinflammation in brain regions associated with memory, and improved HH-induced cognitive impairments by modulating the cyclic adenosine monophosphate response element-binding protein/brain-derived neurotrophic factor signaling pathway. Higher doses generally yielded more effective outcomes than lower doses. QEE also significantly reshaped the gut microbiome structure of HH mice, inhibited gut barrier damage, and reduced lipopolysaccharide migration, thereby increasing short-chain fatty acids (SCFAs) levels. Our findings suggest that QEE may be a promising strategy for preventing hypoxia-induced cognitive impairments by maintaining gut microbiome stability and increasing SCFAs levels.

Whole-genome sequence analysis of SFTS bunyavirus in Huzhou, China

Severe fever with thrombocytopenia syndrome (SFTS), a tick-borne emerging infectious disease caused by SFTS virus (SFTSV), is a growing public health threat due to its high mortality rate. To understand the genomic characteristics of SFTSV samples isolated in Huzhou, China, the full-length genomes of Huzhou SFTSV isolates obtained between February 1, 2019 and December 30, 2023 were sequenced, and the gene loci, evolution, and sequence identity of the genome sequences were analyzed using MEGA. The complete genome sequences of seven SFTSV samples were obtained successfully. The full-length genome of each isolate was 11 490 bp in length, composed of a large (L) segment of 6368 bp, medium (M) segment of 3378 bp, and small (S) segment of 1744 bp. The SFTSV samples isolated in Huzhou belonged to multiple genotypes, but were mainly of type D. Each subtype showed nucleotide sequence and amino acid sequence identities of more than 93.67% and 97.18%, respectively, with the syngeneic human host reference strain and more than 93.67% and 97.76%, respectively, with the syngeneic tick-derived host reference strain. Nucleotide sequence analysis of SFTSV isolates from Huzhou showed mutations in genes on all three segments, with those on the M segment showing the highest mutation rate. The nucleotide variations were mainly base transversions. Further studies of the distribution of SFTSV genotypes, sites of nucleotide mutations, and amino acid variations are required.

Factors Affecting Phage-Bacteria Coevolution Dynamics

Bacteriophages (phages) have coevolved with their bacterial hosts for billions of years. With the rise of antibiotic resistance, the significance of using phages in therapy is increasing. Investigating the dynamics of phage evolution can provide valuable insights for pre-adapting phages to more challenging clones of their hosts that may arise during treatment. Two primary models describe interactions in phage-bacteria systems: arms race dynamics and fluctuating selection dynamics. Numerous factors influence which dynamics dominate the interactions between a phage and its host. These dynamics, in turn, affect the coexistence of phages and bacteria, ultimately determining which organism will adapt more effectively to the other, and whether a stable state will be reached. In this review, we summarize key findings from research on phage-bacteria coevolution, focusing on the different concepts that can describe these interactions, the factors that may contribute to the prevalence of one model over others, and the effects of various dynamics on both phages and bacteria.

Ontogenetic Analysis of Chelonus formosanus and Diversity of Its Internal Microbiota

Chelonus formosanus is a parasitic wasp capable of parasitizing various Noctuidae pests, including the highly invasive Spodoptera frugiperda, and it demonstrates strong pest control potential. Both egg and larval stages primarily occur within the host organism, and the total developmental time from egg to adult is approximately 19.62 days. To investigate the microbial communities at different stages, we performed 16S rDNA sequencing (V1-V9 region) using PacBio sequencing and identified 404 bacterial species belonging to 61 classes, 116 orders, 182 families, and 308 genera across larval, pupal, female, and male adult stages. Bacterial diversity and richness varied across the stages, with Enterobacter and Enterococcus dominating in larvae and pupae and Pseudomonas emerging as dominant in female adults. In contrast, male adults predominantly resided with Ralstonia and Achromobacter. The predicted functions of bacteria within C. formosanus at different developmental stages are predominantly marked by the high abundance of metabolic pathways. This study provides a comprehensive understanding of the morphology of C. formosanus and contributes to the practical control of host pests. Additionally, our findings preliminarily characterized the microbial community of various developmental stages, laying the groundwork for its functional study.

Validation methods for encapsulated faecal microbiota transplantation: a scoping review

Faecal microbiota transplantation (FMT) is increasingly used for diseases associated with a disrupted intestinal microbiome, mainly Clostridioides difficile infection. Encapsulated FMT is a patient-friendly application method that improves accessibility and convenience. Capsule processing may be standardised, but validation protocols are warranted. This review aimed to describe published validation methods for encapsulated FMT. Original studies reporting using encapsulated faecal formulations were included, regardless of indication. Studies were excluded if they did not address processing and validation or used non-donor-derived content. We conducted a comprehensive scoping review, implementing a systematic search strategy in PubMed, Embase and Web of Science. Processing data and validation methods were registered during full-text analysis and combined to create an overview of approaches for assessing quality in encapsulated FMT processing. The searches identified 324 unique studies, of which 44 were included for data extraction and analysis. We identified eight validation covariables: donor selection, pre-processing, preservation, oxygen-sparing processing, microbial count, viability, engraftment and clinical effect outcomes, from which we constructed a model for quality assessment of encapsulated FMT that exhaustively categorised processing details and validation measures. Our model comprised three domains: (1) Processing (donor selection and processing protocol), (2) Content analysis (microbiota measures and dose measures) and (3) Clinical effect (engraftment and clinical outcomes). No studies presented a reproducible capsule protocol; their validation strategies were sparse and divergent. The validation of FMT capsules is heterogeneous, and processing requires relevant standardisation protocols, mainly focusing on capsule content. Future studies should report validation covariables to enable accurate comparative assessments of clinical effects.

Lung Microbiota: From Healthy Lungs to Development of Chronic Obstructive Pulmonary Disease

Lung health is dependent on a complex picture of the lung microbiota composed of bacteriobiota, mycobiota, and virome. The studies have demonstrated that the lung microbiota has a crucial role in host protection by regulating innate and adaptive lung immunity. Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disease featuring changed microbiota composition and diversity, known as a dysbiosis. The lung dysbiosis increases with the progress of COPD and during exacerbation. Two models of dysbiosis have been proposed: dysbiosis and inflammation cycles and the disturbance of bacterial interactome. Still, it is unknown if the driving factor of the pathogenesis of COPD belongs to the host or microbiota. Recently, host-microbiota and microbe-microbe interactions have been highlighted in COPD, but the mechanisms behind these interactions need further exploration. The function of the gut-lung axis is crucial for the maintenance of lung health and is affected in COPD. The application of probiotics has resulted in host-beneficial effects, and it is likely that future progress in this field will aid in the therapy of COPD. In this review, the composition of the lung microbiota, molecular mechanisms, and clinical aspects relating to host and microbiota in health and COPD are comprehensively provided.

Microbiota-Gut-Brain Axis: Mass-Spectrometry-Based Metabolomics in the Study of Microbiome Mediators-Stress Relationship

The microbiota-gut-brain axis is a complex bidirectional communication system that involves multiple interactions between intestinal functions and the emotional and cognitive centers of the brain. These interactions are mediated by molecules (metabolites) produced in both areas, which are considered mediators. To shed light on this complex mechanism, which is still largely unknown, a reliable characterization of the mediators is essential. Here, we review the most studied metabolites in the microbiota-gut-brain axis, the metabolic pathways in which they are involved, and their functions. This review focuses mainly on the use of mass spectrometry for their determination, reporting on the latest analytical methods, their limitations, and future perspectives. The analytical strategy for the qualitative-quantitative characterization of mediators must be reliable in order to elucidate the molecular mechanisms underlying the influence of the above-mentioned axis on stress resilience or vulnerability.

Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity

Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica's life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.

The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation

The history of clinical resistance to tetracycline antibiotics is characterized by cycles whereby the deployment of a new generation of drug molecules is quickly followed by the discovery of a new mechanism of resistance. This suggests mechanism-specific selection by each tetracycline generation; however, the evolutionary dynamics of this remain unclear. Here, we evaluate 24 recombinant Escherichia coli strains expressing tetracycline resistance genes from each mechanism (efflux pumps, ribosomal protection proteins, and enzymatic inactivation) in the context of each tetracycline generation. We employ a high-throughput barcode sequencing protocol that can discriminate between strains in mixed culture and quantify their relative abundances. We find that each mechanism is preferentially selected for by specific antibiotic generations, leading to their expansion. Remarkably, the minimum inhibitory concentration associated with individual genes is secondary to resistance mechanism for inter-mechanism relative fitness, but it does explain intra-mechanism relative fitness. These patterns match the history of clinical deployment of tetracycline drugs and resistance discovery in pathogens.

Genome assembly of Hawaiian flower thrips Thrips hawaiiensis (Thysanoptera: Thripidae)

The Hawaiian flower thrips, Thrips hawaiiensis, is a common flower inhabiting pest of various horticultural plant species. It damages flowers and fruits by puncturing. T. hawaiiensis shows a rapidly developed resistance to chemical control. The lack of a high-quality reference genome limits our understanding of the genetics of T. hawaiiensis. Here, we sequenced the genome of T. hawaiiensis using Oxford Nanopore sequencing technology, Illumina, and Hi-C technology, yielding a genome assembly of 287.59 Mb with scaffold N50 of 13.84 Mb. BUSCO analysis demonstrated the T. hawaiiensis genome assembly has a high-level completeness of 98.7%. In total, 18,289 protein-coding genes were annotated and 26.69% of the genome were annotated as repeats. Our study presents the first high-quality genome assembly of T. hawaiiensis and lays the foundation for further studies on thrips genetic characteristics and pest management.

Linking molecular mechanisms to their evolutionary consequences: a primer

A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties-the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation-can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes.

Nutrients and Nutraceuticals from Vitis vinifera L. Pomace: Biological Activities, Valorization, and Potential Applications

Grape pomace, also known as wine pomace, is a by-product of winemaking that has traditionally been discarded. However, recent studies have highlighted its rich nutritional and bioactive potential, positioning it as a promising resource for various applications in the functional food, pharmaceutical, and cosmetic sectors. This review explores the nutrient and nutraceutical contents of grape pomace, including its high levels of polyphenols, dietary fiber, vitamins, minerals, and melatonin. The biological activities of grape pomace, such as antioxidant, anti-inflammatory, antimicrobial, and anticancer effects, are also discussed, emphasizing its potential as raw material endowed with multifunctional properties. Additionally, the valorization of grape pomace as a food supplement and for the development of cosmetics is examined, focusing on its incorporation into dietary products and skincare formulations. The growing interest in the sustainable utilization of grape pomace is underscored, highlighting its significant role in promoting human health and contributing to a circular economy.

IL-21 and anti-α4β7 dual therapy during ART promotes immunological and microbiome responses in SIV-infected macaques

Despite combination antiretroviral therapy (ART), HIV causes persistent gut barrier dysfunction, immune depletion, and dysbiosis. Furthermore, ART interruption results in reservoir reactivation and rebound viremia. Both IL-21 and anti-α4β7 improve gut barrier functions, and we hypothesized that combining them would synergize as a dual therapy to improve immunological outcomes in SIV-infected rhesus macaques (RMs). We found no significant differences in CD4+ T cell reservoir size by intact proviral DNA assay. SIV rebounded in both dual-treated and control RMs following analytical therapy interruption (ATI), with time to rebound and initial rebound viremia comparable between groups; however, dual-treated RMs showed slightly better control of viral replication at the latest time points after ATI. Additionally, following ATI, dual-treated RMs showed immunological benefits, including T cell preservation and lower PD-1+ central memory T cell (TCM) frequency. Notably, PD-1+ TCMs were associated with reservoir size, which predicted viral loads (VLs) after ATI. Finally, 16S rRNA-Seq revealed better recovery from dysbiosis in treated animals, and the butyrate-producing Firmicute Roseburia predicted PD-1-expressing TCMs and VLs after ATI. PD-1+ TCMs and gut dysbiosis represent mechanisms of HIV persistence and pathogenesis, respectively. Therefore, combining IL-21 and anti-α4β7 may be an effective therapeutic strategy to improve immunological outcomes for people with HIV.

Probiotics Prescribed With Helicobacter pylori Eradication Therapy in Europe: Usage Pattern, Effectiveness, and Safety. Results From the European Registry on Helicobacter pylori Management (Hp-EuReg)

INTRODUCTION

To evaluate the prescription patterns, effectiveness, and safety of adding probiotics to Helicobacter pylori eradication therapy, in Europe.

METHODS

International, prospective, noninterventional registry of the clinical practice of the European gastroenterologists. Data were collected and quality reviewed until March 2021 at AEG-REDCap. The effectiveness was evaluated by modified intention-to-treat analysis, differentiating by geographic areas. Adverse events (AEs) were categorized as mild, moderate, and severe.

RESULTS

Overall, 36,699 treatments were recorded, where 8,233 (22%) were prescribed with probiotics. Probiotics use was associated with higher effectiveness in the overall analysis (odds ratio [OR] 1.631, 95% confidence interval [CI] 1.456-1.828), as well as in triple (OR 1.702, 95% CI 1.403-2.065), quadruple (OR 1.383, 95% CI 0.996-1.920), bismuth quadruple (OR 1.248, 95% CI 1.003-1.554), and sequential therapies (OR 3.690, 95% CI 2.686-5.069). Lactobacillus genus was associated with a higher therapy effectiveness in Eastern Europe when triple (OR 2.625, 95% CI 1.911-3.606) and bismuth quadruple (OR 1.587, 95% CI 1.117-2.254) first-line therapies were prescribed. In Central Europe, the use of probiotics was associated with a decrease in both the overall incidence of AEs (OR 0.656, 95% CI 0.516-0.888) and severe AEs (OR 0.312, 95% CI 0.217-0.449). Bifidobacterium genus was associated with lower overall (OR 0.725, 95% CI 0.592-0.888) and severe (OR 0.254, 95% CI 0.185-0.347) AEs, and Saccharomyces was associated with reduced overall (OR 0.54, 95% CI 0.32-0.91) and severe (OR 0.257, 95% CI 0.123-0.536) AEs under quadruple-bismuth regimen.

DISCUSSION

In Europe, the use of probiotics was associated with higher effectiveness and safety of H. pylori eradication therapy. Lactobacillus improved treatment effectiveness, whereas Bifidobacterium and Saccharomyces were associated with a better safety profile.

Innate Immunity in Insects: The Lights and Shadows of Phenoloxidase System Activation

Melanogenesis and melanin deposition are processes essential for the effective immune response of insects to various invaders. Phenoloxidase (PO), produced in specialized cells as an inactive precursor prophenoloxidase (proPO), is the key enzyme for melanin formation. The precursor is activated via limited proteolysis by a dedicated serine proteinase, which is the final element in the cascade of serine proteinases (SPs) that make up the PO system. Melanogenesis provides different cytotoxic molecules active in fighting infections, as well as melanin, which is important for sequestration of invaders. However, since the cytotoxic reactive compounds generated during melanization also pose a threat to host cells, strict control of the PO system is necessary for host self-protection. Different pathogens and parasites influence the PO system and melanization through various strategies, which allow them to survive and develop in the host insect body. In this review, we characterize "the lights and shadows" of PO system activation, indicating, on one hand, its advantages as an efficient and effective mechanism of the insect immune response and, on the other hand, the dangers for the insect host associated with the improper functioning of this system and selected strategies for regulating its activity by entomopathogenic organisms.

Protein Quality Control is a Master Modulator of Molecular Evolution in Bacteria

The bacterial protein quality control (PQC) network comprises a set of genes that promote proteostasis (proteome homeostasis) through proper protein folding and function via chaperones, proteases, and protein translational machinery. It participates in vital cellular processes and influences organismal development and evolution. In this review, we examine the mechanistic bases for how the bacterial PQC network influences molecular evolution. We discuss the relevance of PQC components to contemporary issues in evolutionary biology including epistasis, evolvability, and the navigability of protein space. We examine other areas where proteostasis affects aspects of evolution and physiology, including host-parasite interactions. More generally, we demonstrate that the study of bacterial systems can aid in broader efforts to understand the relationship between genotype and phenotype across the biosphere.

Skin microbiome and dermatologic disorders

Human skin acts as a physical barrier to prevent the entry of pathogenic microbes while simultaneously providing a home for commensal bacteria and fungi. Microbiome sequencing studies have demonstrated the unappreciated diversity and selectivity of these microbes. Functional studies have demonstrated the impact of specific strains to tune the immune system, sculpt the microbial community, provide colonization resistance, and promote epidermal barrier integrity. Recent studies have integrated the microbiome, immunity, and tissue integrity to understand their interplay in common disorders such as atopic dermatitis. In this Review, we explore microbiome shifts associated with cutaneous disorders with an eye toward how the microbiome can be mined to identify new therapeutic opportunities.

Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles

Beetles that feed on the nutritionally depauperate and recalcitrant tissues provided by the leaves, stems, and roots of living plants comprise one-quarter of herbivorous insect species. Among the key adaptations for herbivory are plant cell wall-degrading enzymes (PCWDEs) that break down the fastidious polymers in the cell wall and grant access to the nutritious cell content. While largely absent from the non-herbivorous ancestors of beetles, such PCWDEs were occasionally acquired via horizontal gene transfer (HGT) or by the uptake of digestive symbionts. However, the macroevolutionary dynamics of PCWDEs and their impact on evolutionary transitions in herbivorous insects remained poorly understood. Through genomic and transcriptomic analyses of 74 leaf beetle species and 50 symbionts, we show that multiple independent events of microbe-to-beetle HGT and specialized symbioses drove convergent evolutionary innovations in approximately 21,000 and 13,500 leaf beetle species, respectively. Enzymatic assays indicate that these events significantly expanded the beetles' digestive repertoires and thereby contributed to their adaptation and diversification. Our results exemplify how recurring HGT and symbiont acquisition catalyzed digestive and nutritional adaptations to herbivory and thereby contributed to the evolutionary success of a megadiverse insect taxon.

'Drifting' Buchnera genomes track the microevolutionary trajectories of their aphid hosts

Evolution of Buchnera-aphid host symbioses is often studied among species at macroevolutionary scales. Investigations within species offer a different perspective about how eco-evolutionary processes shape patterns of genetic variation at microevolutionary scales. Our study leverages new and publicly available whole-genome sequencing data to study Buchnera-aphid host evolution in Myzus persicae, the peach potato aphid, a globally invasive and polyphagous pest. Across 43 different asexual, clonally reproducing isofemale strains, we examined patterns of genomic covariation between Buchnera and their aphid host and considered the distribution of mutations in protein-coding regions of the Buchnera genome. We found Buchnera polymorphisms within aphid strains, suggesting the presence of genetically different Buchnera strains within the same clonal lineage. Genetic distance between pairs of Buchnera samples was positively correlated to genetic distance between their aphid hosts, indicating shared evolutionary histories. However, there was no segregation of genetic variation for both M. persicae and Buchnera with plant host (Brassicaceae and non-tobacco Solanaceae) and no associations between genetic and geographic distance at global or regional spatial scales. Abundance patterns of non-synonymous mutations were similar to synonymous mutations in the Buchnera genome, and both mutation classes had similar site frequency spectra. We hypothesize that a predominance of neutral processes results in the Buchnera of M. persicae to simply 'drift' with the evolutionary trajectory of their aphid hosts. Our study presents a unique microevolutionary characterization of Buchnera-aphid host genomic covariation across multiple aphid clones. This provides a new perspective on the eco-evolutionary processes generating and maintaining polymorphisms in a major pest aphid species and its obligate primary endosymbiont.

RNA virus diversity highlights the potential biosecurity threat posed by Antarctic krill

Antarctic krill Euphausia superba, one of the most abundant species on the planet, is a keystone species of the Southern Ocean ecosystem. In the present study, we analyzed the RNA virome of Antarctic krill via metatranscription methods. The results showed that only 0.39% (49/12, 558) of the resultant unigenes could be assigned to known viral taxa, which were most similar to 17 known viruses, including nine invertebrate viruses, two vertebrate viruses, three protozoan viruses and three mycoviruses. However, most of the detected viruses possessed low amino acid similarity with counterparts in the viral databases. Penaeus vannamei picornavirus (PvPV; Family Picornaviridae) and covert mortality nodavirus (CMNV; Family Nodaviridae) were the two most abundant viruses in the Antarctic krill RNA virome. Notably, PvPV and CMNV are known pathogens to multiple aquatic animals according to epidemiological survey and exposure experiments, whereby PvPV positive krill caused clinical symptoms and histopathological lesions to P. vannamei and similarly, CMNV infection altered the swimming and feeding behavior of parent marine medaka Oryzias melastigma and caused tissue damage and even spinal curvature of the offspring. Results herein reveal, for the first time, the high abundance and taxonomic diversity of viruses in Antarctic krill while simultaneously highlighting the risk of an important virus reservoir to global aquaculture, and the potential impact on animals in the Antarctic ecosystem.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00270-w.

Exploring the Multifaceted Therapeutic Potential of Probiotics: A Review of Current Insights and Applications

The interplay between human health and the microbiome has gained extensive attention, with probiotics emerging as pivotal therapeutic agents due to their vast potential in treating various health issues. As significant modulators of the gut microbiota, probiotics are crucial in maintaining intestinal homeostasis and enhancing the synthesis of short-chain fatty acids. Despite extensive research over the past decades, there remains an urgent need for a comprehensive and detailed review that encapsulates probiotics' latest insights and applications. This review focusses on the multifaceted roles of probiotics in promoting health and preventing disease, highlighting the complex mechanisms through which these beneficial bacteria influence both gut flora and the human body at large. This paper also explores probiotics' neurological and gastrointestinal applications, focussing on their significant impact on the gut-brain axis and their therapeutic potential in a broad spectrum of pathological conditions. Current innovations in probiotic formulations, mainly focusing on integrating genomics and biotechnological advancements, have also been comprehensively discussed herein. This paper also critically examines the regulatory landscape that governs probiotic use, ensuring safety and efficacy in clinical and dietary settings. By presenting a comprehensive overview of recent studies and emerging trends, this review aims to illuminate probiotics' extensive therapeutic capabilities, leading to future research and clinical applications. However, besides extensive research, further advanced explorations into probiotic interactions and mechanisms will be essential for developing more targeted and effective therapeutic strategies, potentially revolutionizing health care practices for consumers.

Are the counts of Streptococcus mutans and Staphylococcus aureus changed in complete denture wearers carrying denture stomatitis? A systematic review with meta-analyses

STATEMENT OF PROBLEM

Despite the importance of Candida spp. on the etiology of denture stomatitis (DS), information on the role of the bacterial component is still scarce.

PURPOSE

The purpose of this systematic review was to evaluate whether the counts of Staphylococcus aureus and Streptococcus mutans were changed in complete denture wearers diagnosed with Candida-associated DS.

MATERIAL AND METHODS

The literature search was performed in 8 databases and by hand searching. The risk of bias was assessed according to the Newcastle-Ottawa qualifier. Meta-analyses were performed considering the microorganism evaluated (S. aureus or S. mutans) and the collection area (mucosa or dentures). The certainty of evidence was assessed according to the grading of recommendations assessment, development and evaluations (GRADE) criteria.

RESULTS

Participants with DS presented higher counts of S. aureus in the mucosa compared with those from the control group (OR, 3.16 [1.62, 6.15]; P<.001). No significant difference between the groups was observed for samples collected from dentures (OR, 0.73 [0.50, 1.07]; P=.110). Conversely, participants without DS presented higher counts of S. mutans both in the mucosa (OR, 0.19 [0.06, 0.63]; P=.006) and dentures (OR, 0.64 [0.41, 1.0]; P=.050).

CONCLUSIONS

Microbial counts in participants with DS changed as a function of the type of microorganism and collection site. The certainty of evidence ranged from very low to low. The findings reinforce the fact that bacteria also play a relevant role in DS and should be more extensively studied. Such information may be useful to guide further therapies to prevent or control DS.

Intra-host variability of SARS-CoV-2: Patterns, causes and impact on COVID-19

Intra-host viral variability is related to pathogenicity, persistence, drug resistance, and the emergence of new clades. This work reviews the large amount of data on SARS-CoV-2 intra-host variability accumulated to date, addressing known and potential implications in COVID-19 and the emergence of VOCs and lineage-defining mutations. Topics covered include the distribution of intra-host polymorphisms across the genome, the corresponding mutational signatures, their patterns of emergence and extinction throughout infection, and the processes governing their abundance, frequency, and type (synonymous, nonsynonymous, indels, nonsense). Besides, evidence is reviewed that the virus can replicate and mutate in isolation at different anatomical compartments, which may imply that what we have learned from respiratory samples could be part of a broader picture.

Dietary, metabolic and gut microbiota influences on primary ovarian failure: a two-sample Mendelian randomization study

BACKGROUND AND OBJECTIVES

Previous studies have reported there were associations between ovarian function and dietary factors, metabolic factors and gut microbiota. However, it is unclear whether causal associations exist. We aimed to explore the causal relationship of these factors with risk of primary ovarian failure (POF).

METHODS AND STUDY DESIGN

Two-sample Mendelian randomization (MR) analysis was performed to genetically predict the causal effects of dietary and metabolic factors and gut microbiota on POF. The inverse variance weighted (IVW) method was used as the primary statistical method. A series of sensitivity analyses, including weighted median, MR-Egger, simple mode, weighted mode methods, and leave-one-out analysis, were conducted to assess the robustness of the MR analysis results.

RESULTS

IVW analysis revealed that cigarettes smoked per day, coffee intake and cooked vegetable intake were not causally correlated with POF at the genetic level. However, POF were associated with fresh fruit intake, BMI, Eubacterium (hallii group), Eubacterium (ventriosum group), Adlercreutzia, Intestinibacter, Lachnospiraceae (UCG008), and Terrisporobacter. These findings were robust according to extensive sensitivity analyses.

CONCLUSIONS

This study identified several dietary factors, metabolic factors and gut microbiota taxa that may be causally implicated in POF, potentially offering new therapeutic targets.

Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome

The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.

Regulation of melanization in aphids by parasitoid wasp venom proteins enhances mummification

BACKGROUND

Interactions between parasitic insects and their hosts demonstrate the complexity of evolutionary processes. Specifically, the parasitoid wasp Aphidius ervi manipulates its host, the pea aphid Acyrthosiphon pisum, through strategic venom injection to enhance mummification. This study explores how this venom affects the aphid's immune system, particularly targeting the activity of the phenoloxidase (PO) enzyme.

RESULTS

Following the injection of venom from A. ervi, significant changes were observed in the expression of immune-related genes in A. pisum, especially notable expression changes of ApPPOs and a reduction of PO activity. Multi-omics sequencing identified 74 potential venom proteins in the venom gland of A. ervi, including serine protease homolog 1 (AeSPH1) and serine protease inhibitor (AeSPN1), hypothesized to regulate PO activity. The injection of recombinant protein AeSPH1 and AeSPN1 into the A. pisum hemocoel selectively reduced the expression of ApPPO1, without affecting ApPPO2, and effectively suppressed melanization. Moreover, RNAi targeting AeSPH1 significantly reduced the mummification rate in A. pisum population parasitized by A. ervi.

CONCLUSION

Our findings clarify the complex biochemical mechanisms underlying host-wasp interactions and highlight potential avenues for developing targeted biological control strategies. © 2024 Society of Chemical Industry.

Defensive Symbiont Genotype Distributions Are Linked to Parasitoid Attack Networks

Facultative symbionts are widespread in arthropods and can provide important services such as protection from natural enemies. Yet what shapes associations with defensive symbionts in nature remains unclear. Two hypotheses suggest that interactions with either antagonists or host plants explain the prevalence of symbionts through shared selective pressures or vectors of symbiont transmission. Here we investigate the factors determining similarities in the Hamiltonella defensa symbiosis shared amongst field-collected aphid species. After accounting for host species relatedness, we find that Hamiltonella's genotype distribution aligns with sharing the same parasitoids, rather than host plants, highlighting parasitoids and hosts as key selective agents shaping the symbiosis across aphid species. Our data indicates parasitoid host specificity drives the prevalence of specific aphid-Hamiltonella associations, suggesting defensive symbioses are maintained by the selective pressure imposed by dominant parasitoids and their aphid hosts. These findings underscore the importance of interactions with natural enemies in explaining patterns of defensive symbiosis in nature.

Effect of docosahexaenoic acid as an anti-inflammatory for Caco-2 cells and modulating agent for gut microbiota in children with obesity (the DAMOCLE study)

PURPOSE

Docosahexaenoic acid (DHA) is a long-chain omega-3 polyunsaturated fatty acid. We investigated the dual health ability of DHA to modulate gut microbiota in children with obesity and to exert anti-inflammatory activity on human intestinal Caco-2 cells.

METHODS

In a pilot study involving 18 obese children (8-14 years), participants received a daily DHA supplement (500 mg/day) and dietary intervention from baseline (T0) to 4 months (T1), followed by dietary intervention alone from 4 months (T1) to 8 months (T2). Fecal samples, anthropometry, biochemicals and dietary assessment were collected at each timepoint. At preclinical level, we evaluated DHA's antioxidant and anti-inflammatory effects on Caco-2 cells stimulated with Hydrogen peroxide (H2O2) and Lipopolysaccharides (LPS), by measuring also Inducible nitric oxide synthase (iNOS) levels and cytokines, respectively.

RESULTS

Ten children were included in final analysis. No major changes were observed for anthropometric and biochemical parameters, and participants showed a low dietary compliance at T1 and T2. DHA supplementation restored the Firmicutes/Bacteroidetes ratio that was conserved also after the DHA discontinuation at T2. DHA supplementation drove a depletion in Ruminococcaceae and Dialisteraceae, and enrichment in Bacteroidaceae, Oscillospiraceae, and Akkermansiaceae. At genus level, Allisonella was the most decreased by DHA supplementation. In Caco-2 cells, DHA decreased H2O2-induced reactive oxygen species (ROS) and nitric oxide (NO) production via iNOS pathway modulation. Additionally, DHA modulated proinflammatory (IL-1β, IL-6, IFN-γ, TNF-α) and anti-inflammatory (IL-10) cytokine production in LPS-stimulated Caco-2 cells.

CONCLUSION

An improvement in gut dysbiosis of children with obesity seems to be triggered by DHA and to continue after discontinuation. The ability to modulate gut microbiota, matches also with an anti-inflammatory effect of DHA on Caco-2 cells.

Detection of colorectal-cancer-associated bacterial taxa in fecal samples using next-generation sequencing and 19 newly established qPCR assays

We have previously identified increased levels of distinct bacterial taxa within mucosal biopsies from colorectal cancer (CRC) patients. Following prior research, the aim of this study was to investigate the detection of the same CRC-associated bacteria in fecal samples and to evaluate the suitability of fecal samples as a non-invasive material for the detection of CRC-associated bacteria. Next-generation sequencing (NGS) of the 16S ribosomal RNA (rRNA) V4 region was performed to evaluate the detection of the CRC-associated bacteria in the fecal microbiota of cancer patients, patients with adenomatous polyp and healthy controls. Furthermore, 19 novel species-specific quantitative PCR (qPCR) assays were established to detect the CRC-associated bacteria. Approximately, 75% of the bacterial taxa identified in biopsies were reflected in fecal samples. NGS failed to detect low-abundance CRC-associated taxa in fecal samples, whereas qPCR exhibited high sensitivity and specificity in identifying all targeted taxa. Comparison of fecal microbial composition between the different patient groups showed enrichment of Fusobacterium nucleatum, Parvimonas micra, and Gemella morbillorum in cancer patients. Our findings suggest that low-abundance mucosa-associated bacteria can be detected in fecal samples using sensitive qPCR assays.

Prevalence of Heritable Symbionts in Parisian Bedbugs (Hemiptera: Cimicidae)

Like many insects, the biology of bedbugs is impacted by a range of partner heritable microbes. Three maternally inherited symbionts are recognised: Wolbachia (an obligate partner), Symbiopectobacterium purcellii strain SyClec, and Candidatus Tisiphia sp. (facultative symbionts typically present in some but not all individuals). Past work had examined the presence of these heritable microbes from established laboratory lines, but not from broader field samples. We therefore deployed targeted endpoint PCR assays to determine the symbiont infection status for 50 bedbugs collected from 10 districts of Paris during the 2023 outbreak. All three symbionts were found to be broadly present across Cimex lectularius samples, with the Symbiopectobacterium-Candidatus Tisiphia-Wolbachia triple infection most commonly observed. A minority of individuals lacked either one or both facultative symbionts. Five mtDNA haplotypes were observed across the COI barcode region, and triple infections were found in all mtDNA haplotypes, indicating that symbiont infection is not a recent invasion event. We conclude that the Parisian bedbug outbreak was one in which the host's secondary symbionts were present at high-frequency coinfections, and facultative symbionts are an important but uncharacterised component of bedbug populations.

Neglected Human Risk Factors Determining Sustainable Health by Microbial Causes: Individual Versus Social Conducts, Scientific Versus Stultified Behaviour

Microbes constitute a ubiquitous warp, a highly sensitive skin of the biosphere that can be scratched and damaged by all human activities. However, the existence of life in general and the human species, in particular, depends on the intelligent preservation of such a biological microbiological cement linking our health with the health of Earth. We are responsible for maintaining sustainable health by managing our damaging individual and social behaviour, and we are also charged with the duty of correcting the microbial disequilibrium we are provoking. The harmful secondary effects resulting from the nature of the species Homo sapiens are frequently neglected. However, sustainable health by microbial causes depends on our individual and social psychology. The role of individual psychology, social behaviour (including the 'tragedy of the commons'), based on collective psychology, culture, values and social norms, and the influence on sustainable health of the methodology of research and management of interventions are briefly analysed. As a general antidote to our unavoidable natural stultified behaviour, education in science is the only possibility to counteract mistakes and restore human dignity.