Effects of adaptation to crowded larval environment on the evolution of sperm competitive ability in males of Drosophila melanogaster

Two of the most important environmental factors that affect the sperm competitive ability in males are the availability of resources and the socio-sexual environment. Numerous studies have investigated the individual effects of these factors, but their combined effect on the evolution of sperm competitive ability remains untested. A crowded larval environment is unique because it simultaneously affects the fitness of the organism through both resource availability and the socio-sexual environment. In this study, we used a set of four laboratory populations of D. melanogaster, evolved under a crowded larval environment for more than 165 generations and their respective controls to investigate how the sperm competitive ability of the males is affected by a single generation of larval crowding versus evolution under a crowded larval environment for more than 165 generations. Our results show that larval crowding negatively affects the sperm defence ability of males evolved in a crowded larval environment, while it has no effect on the sperm defence ability of control males. Additionally, larval crowding negatively impacts the sperm offence ability in both control and evolved populations. Males from populations adapted to a crowded larval environment exhibit lower sperm offence ability at an older age compared to control populations.

Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic morphine

The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for drug dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance, which could be influenced by differences in microbiota, and yet no study design has capitalized upon this natural variation. We leveraged natural behavioral variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained sustained antinociception. Mice that did not develop tolerance maintained a higher capacity for production of the short-chain fatty acid (SCFA) butyrate known to bolster intestinal barriers and promote neuronal homeostasis. Both fecal microbial transplantation (FMT) from donor mice that did not develop tolerance and dietary butyrate supplementation significantly reduced the development of tolerance independently of suppression of systemic inflammation. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.

Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism

The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.

Microbial succinate promotes the response to metformin by upregulating secretory immunoglobulin a in intestinal immunity

Metformin is the first-line pharmacotherapy for type 2 diabetes mellitus; however, many patients respond poorly to this drug in clinical practice. The potential involvement of microbiota-mediated intestinal immunity and related signals in metformin responsiveness has not been previously investigated. In this study, we successfully constructed a humanized mouse model by fecal transplantation of the gut microbiota from clinical metformin-treated - responders and non-responders, and reproduced the difference in clinical phenotypes of responsiveness to metformin. The abundance of Bacteroides thetaiotaomicron, considered a representative differential bacterium of metformin responsiveness, and the level of secretory immunoglobulin A (SIgA) in intestinal immunity increased significantly in responder recipient mice following metformin treatment. In contrast, no significant alterations in B. thetaiotaomicron and SIgA were observed in non-responder recipient mice. The study of IgA-/- mice confirmed that downregulated expression or deficiency of SIgA resulted in non-response to metformin, meaning that metformin was unable to improve dysfunctional glucose metabolism and reduce intestinal and adipose tissue inflammation, ultimately leading to systemic insulin resistance. Furthermore, supplementation with succinate, a microbial product of B. thetaiotaomicron, potentially reversed the non-response to metformin by inducing the production of SIgA. In conclusion, we demonstrated that upregulated SIgA, which could be regulated by succinate, was functionally involved in metformin response through its influence on immune cell-mediated inflammation and insulin resistance. Conversely, an inability to regulate SIgA may result in a lack of response to metformin.

Gut microbial dysbiosis associated to diarrheic irritable bowel syndrome can be efficiently simulated in the Mucosal ARtificial COLon (M-ARCOL)

Irritable bowel syndrome (IBS) is a common chronic gastrointestinal disorder, with diarrhea-predominant IBS (IBS-D) as the most frequent subtype. The implication of gut microbiota in the disease's etiology is not fully understood. In vitro gut systems can offer a great alternative to in vivo assays in preclinical studies, but no model reproducing IBS-related dysbiotic microbiota has been developed. Thanks to a large literature review, a new Mucosal ARtifical COLon (M-ARCOL) adapted to IBS-D physicochemical and nutritional conditions was set-up. To validate the model and further exploit its potential in a mechanistic study, in vitro fermentations were performed using bioreactors inoculated with stools from healthy individuals (n = 4) or IBS-D patients (n = 4), when the M-ARCOL was set-up under healthy or IBS-D conditions. Setting IBS-D parameters in M-ARCOL inoculated with IBS-D stools maintained the key microbial features associated to the disease in vivo, validating the new system. In particular, compared to the healthy control, the IBS-D model was characterized by a decreased bacterial diversity, together with a lower abundance of Rikenellaceae and Prevotellaceae, but a higher level of Proteobacteria and Akkermansiaceae. Of interest, applying IBS-D parameters to healthy stools was not sufficient to trigger IBS-D dysbiosis and applying healthy parameters to IBS-D stools was not enough to restore microbial balance. This validated IBS-D colonic model can be used as a robust in vitro platform for studies focusing on gut microbes in the absence of the host, as well as for testing food and microbiota-related interventions aimed at personalized restoration of gut microbiota eubiosis.

Previous Moraxella catarrhalis Infection as a Risk Factor of COPD Exacerbations Leading to Hospitalization

Haemophilus influenzae (H. influenzae) and Moraxella catarrhalis (M. catarrhalis) are associated with acute exacerbation of chronic obstructive pulmonary disease (AECOPD); however, their role in the pathogenesis of COPD is unknown. We retrospectively analysed the clinical data of patients with AECOPD (modified British Medical Research Council scale score, Global Initiative for Chronic Obstructive Lung Disease [GOLD] classification, pre-admission antibiotic and inhalant usage, sputum culture and epidemic influenza virus antigen test) for association with admission frequency. Among 169 eligible patients, pathogens were and were not detected in 64 and 105, respectively. The GOLD classification grade was higher in the non-detection group with a prior antimicrobial administration rate of 21.9% than in the detection group. H. influenzae and M. catarrhalis, each identified in 24.6% of the total number of detected pathogens, were the most common infectious bacteria. The GOLD classification grade was higher in the re-hospitalisation group than in the one-time hospitalisation group (p < 0.01). Regarding type of pathogen, M. catarrhalis infection (n = 16) was more common in the re-hospitalisation group. History of M. catarrhalis, H. influenzae infection and GOLD grade ≥ III were risk factors for re-hospitalisation, with odds ratios of 92.7 (95% confidence interval [CI]: 3.68-2340.0, p < 0.01), 20.1 (CI: 1.48-274.0, p < 0.05) and 9.83 (CI: 2.33-41.4, p < 0.01), respectively. These bacterial infections and severe airway limitation were associated with increased AECOPD frequency. Routine microbial monitoring may be useful for AECOPD prevention, reducing medical burden and improving prognosis.

Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19

Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.

Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism

The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.

Dynamic reciprocal morphological changes in insect hosts and bacterial symbionts

Symbiotic interactions, central to most life on Earth, are interwoven associations that vary in intimacy and duration. Some of the most well-known examples of symbioses occur between animals and gut bacteria. These associations lead to physiological integration of host and symbionts. The diversity of microbes within animal hosts can make studying them technically challenging. Thus, most science heavily focuses on the animal side of symbioses, limiting study of the microbial symbionts to characterization of their genetic and functional diversity. These limitations are minimized in Heteropteran insects that have specialized midguts that separately house single symbiont species away from ingested food. These insect-bacteria associations allow us to address fundamental questions regarding how both hosts and symbionts change to establish a cooperative relationship. In this study, through ex vivo and in vivo observations of cellular behaviors, we explore concurrent structural and cellular dynamics in both the squash bug host (Anasa tristis) and its Caballeronia zhejiangensis symbionts during the initiation of symbiosis. We elucidate how C. zhejiangensis is sequestered within a specialized symbiotic organ within the A. tristis midgut, how the symbiont uses active motility to reach the symbiotic organ, how symbionts colonize host crypts within the organ and how host crypt morphogenesis progresses during the initiation of symbiotic interactions. Our findings provide insight into how dynamic cellular activity and morphological development reciprocally change in both host and symbiont as they establish symbiotic interactions.

Gut microbiota dysbiosis triggered by salinity stress enhances systemic inflammation in spotted scat (Scatophagus argus)

As an ecological disturbance, salinity changes substantially impact aquatic organism health. Gut microbiota plays a pivotal role in host health and exhibits heightened sensitivity to environmental salinity stress; however, the potential correlative mechanisms between gut microbiota dysbiosis triggered by salinity changes and host health remain unclear. The present study conducted a 4-week stress experiment to investigate the precise impact of gut microbiota on the inflammatory response in Scatophagus argus under different salinities (0 ‰ [hyposaline group, HO], 25 ‰ [control group, CT], and 40 ‰ [hypersaline group, HE]). Our results revealed that both HO and HE stress significantly changed the relative abundances of Gram-negative bacteria and the impairment of intestinal barrier function. Subsequently, the levels of lipopolysaccharide (LPS) in the serum exhibited a significant increase, and the expression levels of genes (tlrs, myd88, irak1, irak4, and traf6) involving TLRs/MyD88/NF-κB signaling pathway and pro-inflammatory cytokines (il-6, il-8, il-1β, and tnf-α) in the representative immune organs were significantly upregulated. Conversely, the abundance of the anti-inflammatory gene (tgf-β1) and its protein contents in serum were decreased. Transplantation of the gut microbiota from S. argus exposed to varying salinities into germ-free Oryzias latipes resulted in an enhanced inflammatory response. Our results suggested that both HO and HE stress increased the presence of Gram-negative bacteria and disrupted the intestinal barrier, leading to elevated serum LPS and subsequent systemic inflammation in fish. These findings provide innovative insights into the influence of salinity manipulation strategies on the health of aquatic organisms, contributing to the mariculture management in coastal areas.

Gut virome: New key players in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing

Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.

Modulation of the Altered Intestinal Microbiota by Use of Antibiotics with a Novel Synbiotic on Wistar Rats

The use of antibiotics unbalances the intestinal microbiota. Probiotics, prebiotics, and synbiotics are alternatives for these unbalances. The effects of a new synbiotic composed of probiotic Saccharomyces boulardii CNCM I-745 and fructans from Agave salmiana (fAs) as prebiotics were assessed to modulate the intestinal microbiota. Two probiotic presentations, the commercial probiotic (CP) and the microencapsulated probiotic (MP) to improve those effects, were used to prepare the synbiotics and feed Wistar rats subjected to antibiotics (AB). Eight groups were studied, including five controls and three groups to modulate the microbiota after the use of antibiotics: G5: AB + MP-synbiotic, G6: AB + CP-synbiotic, and G8: AB + fAs. All treatments were administered daily for 7 days. On days 7 and 21, euthanasia was performed, cecum tissue was recovered and used to evaluate histological analysis and to study microphotograph by TEM, and finally, bacterial DNA was extracted and 16S rRNA gene metabarcode sequencing was performed. Histological analysis showed less epithelial damage and more abundance of the intestinal microbiota in the groups G5, G6, and G8 in comparison with the AB control group after 7 days. Microphotograph of the cecum at 2 weeks post treatment showed that G5 and G6 presented beneficial effects in epithelial reconstruction. Interestingly, in the groups that used the synbiotic without AB (G3 and G4) in addition to contributing to the recovery of the autochthonous microbiota, it promotes the development of beneficial microorganisms; those results were also achieved in the groups that used the synbiotic with AB enhancing the bacterial diversity and regulating the impact of AB.

Exploring the relationship between the gut microbiota and cognitive function in schizophrenia patients with distinct weights

BACKGROUND

The gut microbiota is disrupted in schizophrenia (SZ) patients and is associated with cognitive function. This study aimed to investigate the gut microbiota composition in SZ patients with different body mass index (BMI) levels and their associations with cognitive function.

METHODS

We analyzed 16S rRNA sequencing data from 156 SZ patients, including 88 with overweight/obesity (OW) and 68 with normal weight (NW), and 156 normal control (NC), including 48 with OW and 108 with NW. We analyzed differences in microbial diversity and gut microbiota composition between SZ patients and NC at different BMI levels. Additionally, we explored the correlations between microbial communities, and symptom severity, as well as cognitive function. Furthermore, we examined between-group differences in metabolic pathways.

RESULTS

The abundance of Turicibacter was higher in the SZ_OW group but lower in the SZ_NW group compared to the NC groups at the same BMI level, respectively. In the SZ_OW group, increased Collinsella was significantly negatively associated with cognitive function, whereas decreased Clostridium and Butyricicoccus were significantly positively associated with cognitive function. Additionally, the functional analysis revealed enrichment of "metabolism of other amino acids" and "neurodegenerative disease" pathways, associated with non-standard amino acid metabolism and oxidative stress in the SZ_OW group compared to the NC_OW group.

CONCLUSIONS

Our findings revealed significant differences in the gut microbiota between SZ patients and NC with different BMI levels and identified microbial associations with clinical characteristics, providing new insights into the mechanism of how the gut microbiota could impact cognitive deficits in SZ patients with obesity.

The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure

Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.

Maternal immunoglobulins differentially bind a diverse bacterial community in human colostrum and the stool of breastfed neonates

In the early days, maternal immunoglobulins are essential for sustaining a balanced gut environment by influencing the interaction between the host and the microbiome. The successional establishment of the pioneer strains is an interesting topic of research where maternal immunoglobulins appear to be important. This proof-of-concept study explored the binding pattern of IgA1, IgA2, IgM, and IgG classes to a commensal bacterial in human colostrum and the stool of breastfed neonates. We used flow cytometry coupled with 16S rRNA gene sequencing in human colostrum and neonatal feces samples to characterize this Ig-microbiota association. We observed that in human colostrum samples, IgA2 and IgM bind alfa and beta Proteobacteria, which can potentially stimulate neonatal immune system development in the gut. Other immunoglobulins like IgG predominantly bind facultative anaerobes belonging to the Firmicutes phylum, reported as part of human milk microbiota and pioneer colonizers of the neonatal gut. Maternal immunoglobulins also bind a wide diversity of bacteria in the neonatal stool. For instance, IgA2 and IgM bound more members of the phylum Bacteroidetes in comparison to IgG, these Bacteroidetes and some firmicutes have been reported as late colonizers of the neonatal gut, and their presence is important due to their ability to produce important short chain fatty acids like propionate and butyrate. Our results support the current view that microbial and immunoglobulin transference is crucial for developing the neonate's immune system and individual gut microbiota.

Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis

BACKGROUND

Obesity-related cognitive decline is linked to gut microbiota dysbiosis, with emerging evidence suggesting that dietary interventions may ameliorate cognitive impairment via gut-brain axis modulation. The role of microglial cells in this process remains underexplored.

OBJECTIVE

To investigate how diet-induced changes in gut microbiota influence cognitive function in individuals with obesity and their microglial activity, and to determine the impact of specific dietary interventions.

DESIGN

This study included 96 participants with obesity who were randomised into three dietary intervention groups: Mediterranean diet (Med), alternate-day fasting (ADF) and ketogenic diet (Keto). Cognitive performance and microbiota composition were assessed pre-intervention and post-intervention. The effects of microbiota-related changes on microglial function were further evaluated in mice models through faecal transplantation and in vitro model with microbiota exosome treatment.

RESULTS

Both the Keto and ADF groups demonstrated significant weight loss, but cognitive performance improved most notably in the ADF group, in association with reduced inflammation. Diet-related microbiota composition was correlated with the cognitive outcomes in the human study. Mice models confirmed that the cognitive benefits of ADF were microbiota-dependent and linked to enhanced microglial phagocytic capacity and reduced inflammation, accompanied by changes in microglia morphology.

CONCLUSION

Fasting-induced modifications in gut microbiota contribute to cognitive improvement in individuals with obesity, with microglial cells playing a crucial mediatory role. Among the interventions, ADF most effectively enhanced microglial function and cognitive performance, suggesting its potential as a therapeutic strategy for obesity-related cognitive decline. Further studies are required to fully elucidate the underlying mechanisms.

TRIAL REGISTRATION NUMBER

NCT04453150.

Decoding the Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance

Post-transcriptional tRNA modifications are essential for accurate and efficient protein translation across all organisms. The apicoplast organelle genome of Plasmodium falciparum contains a minimal set of 25 complete tRNA isotypes, making it an ideal model for studying minimal translational machinery. Efficient decoding of mRNA codons by this limited tRNA set depends on post-transcriptional modifications. In this study, we sought to define the minimal set of tRNA-modifying enzymes. Using comparative genomics and apicoplast protein localization prediction tools, we identified 16 nucleus-encoded tRNA-modifying enzymes predicted to localize to the apicoplast. Experimental studies confirmed apicoplast localization for 14 enzymes, including two with dual localization. Combining an apicoplast metabolic bypass parasite line with gene disruption tools, we disrupted 12 of the 14 apicoplast-localized enzymes. Six of these enzymes were found to be essential for parasite survival, and six were dispensable. All six essential enzymes are thought to catalyze modifications in the anticodon loop of tRNAs, and their deletions resulted in apicoplast disruption. Of the two genes refractory to deletion, one exhibited dual localization, suggesting essential functions outside the apicoplast. The other, which appears to localize solely to the apicoplast, may play an indispensable role that is not circumvented by our metabolic bypass. Our findings suggest the apicoplast translation system relies on a minimal set of tRNA modifications concentrated in the anticodon loop. This work advances our understanding of minimal translational machinery in reduced organelles, such as the apicoplast, with promising applications in synthetic biology.

Association between gut microbiota in HIV-infected patients and immune reconstitution following antiretroviral therapy (ART)

BACKGROUND

This study aims to examine the potential link between incomplete immune reconstitution following ART treatment and gut microbiota dysbiosis.

METHODS

We collected clinical data and fecal samples from 50 HIV patients undergoing ART and 30 untreated patients. Based on the observed immune function reconstruction, we further categorized the ART(+) group into a responder group (n = 30) and a non-responder group (n = 20). The gut microbiota composition differences were assessed using Alpha diversity and Beta diversity analysis, while differential genera were identified through linear discriminant analysis effect size (LEfSe). Subsequently, functional disparities in the gut microbiota were investigated using PICRUSt2 and metagenomeSeq software.

RESULTS

The results of Alpha diversity and Beta diversity revealed significant differences in the composition of gut microbiota among the three groups. Differential genus analysis identified Morganella as an exclusive genus present only in the Non-responder group, exhibiting a significantly higher relative abundance. Correlation analysis demonstrated a positive association between Morganella and LDL levels. The CAZY analysis revealed that glycosyltransferase 25 (GT25) was significantly expressed in the Non-responder group, whereas it was either undetectable or exhibited extremely low expression levels in both the Responder group and the ART(-) group. Importantly, the correlation analysis indicated a positive association between Morganella and GT25 secretion.

CONCLUSIONS

The ecological imbalance of Morganella might be associated with incomplete immune reconstitution following ART, potentially mediated by GT25 secretions. Consequently, Morganella could serve as a promising biomarker for predicting incomplete immune reconstitution in AIDS patients undergoing ART.

Role of Microneedles for Improved Treatment of Obesity: Progress and Challenges

Obesity is a global metabolic health epidemic characterized by excessive lipid and fat accumulation, leading to severe conditions such as diabetes, cancer, and cardiovascular disease. Immediate attention and management of obesity-related health risks are most warranted. The imbalance between fat absorption, metabolic rate, and environmental and genetic factors is responsible for obesity. Treatment typically involves lifestyle modifications, pharmacotherapy, and surgery. While lifestyle changes are crucial, effective treatment often necessitates medication as a preferred adjunct strategy. However, medications commonly used, such as oral pharmacotherapy, often show side effects due to systemic exposure and, thus, may not effectively target the intended areas, leading to drug loss. On the other hand, transdermal administration of drugs with microneedle (MN)-based technologies, a painless drug delivery approach with patient compliance, is gaining interest as an alternative obesity treatment, as it directly targets adipose tissue via local delivery, minimizing system exposure and dose reduction. This Review addresses the pathophysiology of obesity, current treatment strategies, challenges in the treatment of obesity using conventional formulations, the importance of the use of nano-based medications through transdermal delivery, and the use of MNs as a promising platform for the effective delivery of nanoparticle-based anti-obesity medications. The potential of combining MNs with stimuli-responsive and non-responsive adjuvant therapies to enhance treatment efficacy and patient outcomes is explored. In addition, the limitations and future perspectives related to the use of MNs for obesity are addressed to highlight the transformative potential of this technology for obesity management. MNs hold promise in precisely delivering anti-obesity drugs while requiring lower dosages and minimizing side effects compared to conventional oral or injectable therapies and ultimately improving the quality of life for individuals struggling with obesity and its associated comorbidities.

A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset

In a given species, genomes and 16S rRNA gene sequences, along with their intragenomic copy numbers, can vary greatly across environments. The gene copy numbers are crucial for technologies which estimate microbial abundances based on gene counts, such as polymerase chain reaction and high-throughput sequencing. In these, taxa with fewer genes may be underestimated, while those with more genes might be overestimated. Therefore, it is essential to have accurate gene copy number databases specific to the niche under study. The 16S rRNA Gene Oral Sequences dataset (16SGOSeq) contains the number of 16S rRNA genes and their variants in the complete genomes of the bacterial and archaeal species present in the human oral cavity. It includes 3,192 complete genomes of oral bacteria and 191 complete genomes of oral archaea, from which the 16S rRNA gene sequences were extracted, and the sequence variants were identified. This oral-specific dataset of prokaryotic organisms and the pipeline followed for its construction can be applied by clinical microbiologists, bioinformaticians, or microbial ecologists in future microbiome research.

Specific dietary fibers steer toward distal colonic saccharolytic fermentation using the microbiota of individuals with overweight/obesity

BACKGROUND

Evidence suggests that increased distal short-chain fatty acid (SCFA) production beneficially impacts metabolic health. However, indigestible carbohydrate availability is limited in the distal colon; consequently, microbes shift toward protein fermentation, often linked to adverse metabolic health effects. We aimed to identify specific fiber(s) that promote saccharolytic fermentation in the distal colon and thereby may (partially) inhibit proteolytic fermentation.

METHODS

Potato-fiber, pectin, and inulin were studied individually and in combination against a high (predigested) protein background using an in vitro model of the colon (TIM-2) inoculated with pooled, standardized fecal microbiota from individuals with overweight/obesity. Microbiota composition and activity were assessed at different timepoints to simulate the travel throughout the colon (proximal: 0-8 h, distal: 8-24 h) and compared to a high protein (HP)_control, receiving only proteins.

RESULTS

Fiber addition increased total SCFA production compared to HP_control (52.11 ± 1.49 vs 27.07 ± 0.26 mmol) whereas total branched-chain fatty acids (BCFA; a marker for protein fermentation) production only slightly decreased (3.31 ± 0.10 vs 4.18 ± 0.40 mmol). Combining potato-fiber and pectin led to the highest total and distal SCFA production and distal SCFA:BCFA. Fiber addition attenuated HP-induced increases in several bacterial taxa including Mogibacterium and Coprococcus, independent of fiber type. Additionally, time- and fiber-specific microbial signatures were identified: inulin increased Bifidobacterium (proximal) relative abundance and pectin and/or potato-fiber increased Prevotella 9 (distal) relative abundance.

CONCLUSION

The most marked increase in distal colonic SCFA production was induced by combining potato-fiber and pectin. Further research should elucidate whether this switch toward saccharolytic fermentation translates into beneficial metabolic health effects in humans.

Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach

INTRODUCTION

The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.

MATERIALS AND METHODS

In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.

RESULTS

Initially, 90 samples were collected, with 20 discarded due to having less than 200 ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p = 0.45) and beta diversity (PERMANOVA R = -0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.

CONCLUSION

Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.

Factors associated with the occurrence of leg ulcers in people with sickle cell disease: A case-control study

AIM

To identify factors associated with the occurrence of leg ulcers in people with sickle cell disease.

METHODS

Unpaired case-control study, conducted in 11 specialized services, between August 2019 and April 2020. The convenience sample consisted of 262 people over 18 years of age, diagnosed with sickle cell disease, with 190 controls and 72 cases. To evaluate the possible factors associated with the occurrence of ulcers, both univariate and multivariate binary logistic regression models were used.

FINDINGS

The factors associated with the occurrence of leg ulcers were previously healed ulcers (odds ratio 48.48), presence of edema in the lower limbs (5.75), use of antibiotics in the last six months (3.08), daily rest (4.59), and use of compression stockings (6.24). Overweight (0.16), physical leisure (0.33), and domestic (0.37) activities were associated with a lower chance of occurrence of ulcers.

CONCLUSION

Identifying the factors that increase the likelihood of leg ulcers occurring in people with sickle cell disease adds to our knowledge of the subject, especially by determining factors that mitigate the occurrence of ulcers and that go beyond clinical variables.

Stabilizing Mutations Enhance Evolvability of BlaC β-lactamase by Widening the Mutational Landscape

Antimicrobial resistance is fueled by the rapid evolution of β-lactamases. However, a gain of new enzyme activity often comes at the expense of reduced protein stability. This evolutionary constraint is often overcome by the acquisition of stabilizing mutations that compensate for the loss of stability invoked by new function mutations. Here, we report three stabilizing mutations (I105F, H184R, and V263I) in BlaC, a serine β-lactamase from Mycobacterium tuberculosis. Using a severely destabilized variant as a template for random mutagenesis and selection, these three mutations emerged together and were able to fully restore resistance toward the antibiotic carbenicillin. In vitro characterization shows that all three mutations increase chemical and thermal stability, which leads to elevated protein levels in the periplasm of Escherichia coli. We demonstrate that the introduction of stabilizing mutations substantially enhances the evolvability of the enzyme. These findings illustrate the important role of stabilizing mutations in enzyme evolution by alleviating function-stability trade-offs and broadening the accessible evolutionary landscape.

Effects of municipal wastewater effluents on the invertebrate microbiomes of an aquatic-riparian food web

Municipal wastewater effluents (MWWEs) contain antimicrobials and other contaminants that can alter the microbiomes of exposed aquatic animals, potentially negatively impacting host health. Contaminants and nutrients from MWWEs may be transferred across the aquatic - riparian boundary by aquatic insects, potentially altering the microbiomes of both prey and consumers. We evaluated host microbiome compositions of several taxa of freshwater larval and adult insects, and riparian spiders at sites upstream and downstream of three wastewater treatment plants. Host microbiome compositions were analyzed by sequencing the 16S rRNA gene and MWWE exposure was assessed using stable carbon (δ13C) and nitrogen (δ15N) isotopes and effluent-associated bacteria. Most downstream insects and riparian spiders were enriched in δ13C and δ15N, indicating exposure to MWWEs and transfer of MWWE-derived nutrients to riparian consumers. Within sites, insect microbiomes varied after metamorphosis with a greater proportion of endosymbionts and effluent-associated bacteria and decreased alpha diversity in adults, and the microbiomes of Tetragnathidae spiders were dominated by endosymbionts (mainly Rickettsia and Wolbachia) compared to all other taxa. Downstream, larval caddisfly (Hydropsychidae) microbiomes had a significantly lower proportion of endosymbionts (Rickettsia) and higher diversity, and Araneidae spiders also had higher diversity. However, there were no significant downstream changes in endosymbiont proportions or alpha diversity of larval and adult chironomids, larval and adult mayflies, larval stoneflies, or Tetragnathidae spiders. Most downstream invertebrates (except larval Chironomidae, adult Diptera, and Tetragnathidae spiders) had altered beta diversity (community compositions); however, host taxonomy explained more of the variation in microbiome composition than site or the interaction between them did. Overall, MWWE bacteria and nutrients were incorporated into most insect larvae and retained throughout metamorphosis, however there were taxa-dependent alterations in downstream insect microbiomes and minimal microbiome alterations to their riparian spider predators.

Cognitive control and consciousness in open biological systems

Thermodynamically open biological systems not only sustain a life-supporting mutual relationship with their environment by exchanging matter and energy but also constantly seek information to navigate probabilistic changes in their surroundings. This work argues that cognition and conscious thought should not be viewed in isolation but rather as parts of an integral control of biological systems to identify and act upon meaningful, semantic information to sustain viability. Under this framework, the development of key cognitive control capacities in centralized nervous systems and the resulting behavior are categorized into distinct Markov decision processes: decision-making with partially observable sensory exteroceptive and interoceptive information, learning and memory, and symbolic communication. It is proposed that the state of conscious thought arises from a control mechanism for speech production resembling actuator control in engineered systems. Also known as the phonological loop, this feedback from the motor to the sensory cortex provides a third type of information flowing into the sensory cortex. The continuous, dissipative loop updates the fleeting working memory and provides humans with an advanced layer of control through a sense of self, agency and perception of flow in time. These capacities define distinct degrees of information fitness in the evolution of information-powered organisms.

Exploring the Mucosal Immune Response in Axial Spondyloarthritis Through Immunoglobulin A-Coated Microbiota

In this review, we focus on the mucosal immune response through Immunoglobulin A (IgA)-coated microbes and their role in gut dysbiosis in axial spondyloarthritis (axSpA) and associated inflammatory bowel disease. IgA-coated microbes contribute significantly to the microbial dysbiosis observed in axSpA, potentially driving gut inflammation and translocating outside of the gut and initiating systemic immune activation, thus contributing to disease pathogenesis. These insights will provide new avenues for understanding and treating axSpA and other immune-mediated inflammatory disorders by targeting specific host immune-microbe interactions.

In vitro human gastrointestinal digestibility and colonic fermentation of edible yeast-based protein: A comparative study with whey and casein

The global protein demand is in constant increase requiring sustainable and healthier alternative proteins for animal and human nutrition. Yeast-based proteins (YBP) represent a non-negligible environmental-friendly fermentation-based solutions with high nutritional quality and bioavailability. Although in vitro studies cannot reflect the full complexity of in vivo digestion, it is considered as useful alternatives to animal models assessing protein digestibility. A 5 h TIM-1 digestion model (TNO Gastro-Intestinal Model) was used to assess the digestibility profile and amino acid bio-accessibility of YBP (3 separate production batches) versus whey and casein as references. Every hour, dialysate and ileal effluent samples were collected. Total nitrogen and free amino acid (FAA) were quantified. To assess the microbial impact, YBP digestate was subjected to 48 h Colon-on-a-Plate batch fermentation, after which the microbial composition by shotgun sequencing and microbial activity by Short-Chain Fatty Acids (SCFAs), Branched-Chain Fatty Acids (BCFAs) (GC-MS) and untargeted metabolomics (LA-REIMS) was analysed (from N = 11 healthy donors of faecal material). YBP, casein and whey were comparable in terms of digestibility. Although YBP showed a different metabolomic fingerprint compared to casein and whey, the microbial activity through SCFA quantification was significantly increased for all proteins compared to blank but not between protein sources. Whey and casein resulted in a higher abundance of Clostridium compared to YBP, while the treatment with YBP resulted in higher abundance of Bacteroides. Altogether, our results suggest that YBP could be a nutritionally relevant alternative protein.

Eating for Optimization: Unraveling the Dietary Patterns and Nutritional Strategies in Endometriosis Management

Endometriosis is a chronic gynecological disorder affecting millions of women worldwide, causing chronic pelvic pain, dyspareunia, dysmenorrhea, and infertility, and severely impacting their quality of life. Treatment primarily involves hormonal therapies and surgical excision, but high recurrence rates and the economic burden are substantial. With these challenges, significant discussion surrounds the potential role of dietary patterns in managing endometriosis, making it necessary to bridge this critical gap. This review investigates the current scientific evidence on the dietary patterns (eg, Mediterranean, vegetarian, anti-inflammatory, low-fermentable oligosaccharides, disaccharides, monosaccharides, and polyols [low-FODMAP], and Western-style diets) associated with endometriosis and provides a concise, yet thorough, overview on the subject. In addition, antioxidants, microbiota, and artificial intelligence (AI) and their potential roles were also evaluated as future directions. An electronic-based search was performed in MEDLINE, Embase, Cochrane Library, CINAHL, ClinicalTrials.gov, Scopus, and Web of Science. The current data on the topic indicate that a diet based on the Mediterranean and anti-inflammatory diet pattern, rich in dietary fiber, omega-3 fatty acids, plant-based protein, and vitamins and minerals, has a positive influence on endometriosis, yielding a promising improvement in patient symptoms. Preclinical investigations and clinical trials indicate that dietary antioxidants and gut microbiota modulation present potential new approaches in managing endometriosis. Also, AI may offer a promising avenue to explore how dietary components interact with endometriosis. Ultimately, considering genetic and lifestyle factors, a healthy, balanced, personalized approach to diet may offer valuable insights on the role of diet as a means of symptom improvement, facilitating the utilization of nutrition for the management of endometriosis.

The four Ws of viruses: Where, Which, What and Why - A deep dive into viral evolution

For centuries, humanity has been captivated by evolution, seeking to unravel the origins of life and identify past patterns with future applications. Viruses, despite their obligate parasitic nature, are the most adaptable biological entities, surpassing cellular life in their variability and adaptability. While many theories about viral evolution exist, a consensus on their origins remains elusive. The quasispecies theory, however, has emerged as a leading framework for understanding viral evolution and, indirectly, their variability and adaptability. This theory illuminates how viruses regulate behaviours such as host range and their symbiotic or antagonistic interactions with hosts. This review delves into the most substantiated theories of viral evolution, addressing four fundamental questions relevant to virus ecology: Where did viruses originate? What factors drive viral evolution? What determines the virus host range? And why do viruses adopt pathogenic or mutualistic strategies? We will provide a comprehensive and up-to-date analysis that integrates diverse theoretical perspectives with empirical data, providing a holistic view of viral evolution and its implications for viral behaviour.

Neuropathogenesis of acute HIV: mechanisms, biomarkers, and therapeutic approaches

PURPOSE OF REVIEW

The neuropathogenesis of acute HIV leads to rapid central nervous system (CNS) involvement, characterized by early viral entry, immune activation, and the formation of viral reservoirs. Despite effective antiretroviral therapy (ART), these reservoirs persist, drive neuroinflammation and injury and lead to HIV-associated neurodegenerative disorders (HAND). This review provides an updated synthesis of the mechanisms in acute HIV neuropathogenesis, biomarkers of CNS injury and emerging therapeutic approaches. A deeper understanding of these mechanisms is critical for addressing persistent HAND in ART-treated individuals.

RECENT FINDINGS

Growing evidence now supports the principal role of infected CD4 + T cells in mediating HIV neuroinvasion alongside monocytes, resulting in seeding in perivascular macrophages, pericytes, and adjacent microglia and astrocytes. These reservoirs contribute to ongoing transcriptional activity and viral persistence despite antiretroviral therapy. Neuroinflammation, driven by activated microglia, astrocytes, inflammasomes, and neurotoxic viral proteins, disrupts neuronal homeostasis. Emerging therapies, including latency-reversing agents and transcription inhibitors, show promise in reducing neuroinflammation and reservoir activity.

SUMMARY

Understanding the mechanisms of HIV neuropathogenesis and reservoir persistence has significant implications for developing targeted therapies to mitigate HAND. Strategies to eliminate CNS reservoirs and reduce neuroinflammation should be prioritized to improve long-term cognitive outcomes in people with HIV.

Deciphering the influence of gut and oral microbiomes on menopause for healthy aging

Menopause is characterized by the cessation of menstruation and a decline in reproductive function, which is an intrinsic component of the aging process. However, it has been a frequently overlooked field of women's health. The oral and gut microbiota, constituting the largest ecosystem within the human body, are important for maintaining human health and notably contribute to the healthy aging of menopausal women. Therefore, a comprehensive review elucidating the impact of the gut and oral microbiota on menopause for healthy aging is of paramount importance. This paper presents the current understanding of the microbiome during menopause, with a particular focus on alterations in the oral and gut microbiota. Our study elucidates the complex interplay between the microbiome and sex hormone levels, explores microbial crosstalk dynamics, and investigates the associations between the microbiome and diseases linked to menopause. Additionally, this review explores the potential of microbiome-targeting therapies for managing menopause-related diseases. Given that menopause can last for approximately 30 years, gaining insights into how the microbiome and menopause interact could pave the way for innovative interventions, which may result in symptomatic relief from menopause and an increase in quality of life in women.

Epiphytic bacterial consortia drive growth regulation in potato under methyl jasmonate elicitation: A leaf surface multi-omics perspective

Methyl jasmonate (MeJA), a lipid-derived signaling molecule widely reported as a plant growth regulator, was revealed in this study to coordinate oxidative stress adaptation and delay senescence in potato through metabolite-microbe interactions, ultimately improving yield. MeJA triggered leaf oxidative stress while integrating rapid enzymatic scavenging, sustained osmoprotectant accumulation, and membrane stabilization, effectively delaying senescence initiation. Metabolic reprogramming under MeJA suppressed endogenous jasmonic acid synthesis while promoting saturated fatty acid biosynthesis, altering leaf surface lipid composition. These lipid changes, combined with MeJA-induced alkaloids, drove functional restructuring of phyllosphere epiphytic bacteria through fatty acid-mediated niche specialization, enhancing bacterial metabolism and enriching stress-resistant Proteobacteria. Notably, the enrichment of saturated fatty acids correlated with microbial taxa exhibiting specialized lipid metabolism. Field trials demonstrated that 200 μmol/L MeJA optimized redox homeostasis and photosynthetic longevity in early-maturing cultivar 'Favorita', translating delayed senescence into significant yield increases. This study proposes a "metabolite-guided microbial niche construction" model, where host lipid metabolism and secondary metabolites jointly shape stress-adapted microbial communities, providing new strategies for precision agrochemical design targeting phyllosphere microbiome engineering.

A novel Erwiniaceae gut symbiont modulates gene expression of the intracellular bacterium Cardinium in the stored product mite Tyrophagus putrescentiae

We examined host and bacterial gene expression profiles in the stored product mite Tyrophagus putrescentiae co-infected with Wolbachia (wTPut) and Cardinium (cTPut) while varying the presence of the Erwiniaceae symbiont (SLS). SLS, a novel symbiont in the family Erwiniaceae, with a genome size of 1.7 Mb, is found in 16% of mite species in infected cultures. In addition, SLS was detected in mite feces but not in their eggs. Although Wolbachia expression remained unchanged, the presence or absence of SLS significantly affected Cardinium expression. It indicated that the effect of Wolbachia on SLS was neutral. In SLS-positive samples, Cardinium exhibited 29 upregulated and 48 downregulated genes compared to SLS-negative samples. Furthermore, Cardinium gene expression strongly correlated with mite KEGG gene expression in SLS-positive samples. Positive Spearman's correlations between Cardinium gene expression and mite KEGG immune and regulatory pathways were doubled in SLS-positive compared to SLS-negative samples. The diversity of expressed genes in the mite host decreased in the presence of SLS. Cardinium had more interacting genes to mite host in SLS-positive samples than without SLS. Transposases are the most affected Cardinium genes, showing upregulation in the presence of SLS. Correlation analyses revealed interactions between Cardinium and SLS via mite immune and regulatory pathways, including lysosome, ubiquitin-mediated proteolysis, PIK3_Akt, and cGMP-PKG. The results showed that Cardinium indirectly affects the gut symbionts of mites.IMPORTANCEThis study introduces a new model to analyze interactions between intracellular bacterial symbionts, gut bacterial symbionts, and their mite hosts. Using gene expression correlations, we investigated how the intracellular Cardinium responds to the novel Erwiniaceae gut symbiont in the mold mite Tyrophagus putrescentiae. The data showed that both mite and Cardinium gene expression are different in the samples with and without Erwiniaceae symbionts. In the presence of Erwiniaceae symbionts, Cardinium increased the interaction with the mite host in terms of changes in gene expression. The mite immune and regulatory pathway gene expression is differently correlated to Cardinium genes in relation to Erwiniaceae symbionts. As a well-known producer of allergens, T. putrescentiae physiology and thus its allergen production are influenced by both symbionts, potentially affecting the release of allergens into human environments.

The evolution of sequence specificity in a DNA binding protein family

Transcriptional regulation enables bacteria to adjust to its environment. This is driven by transcription factors (TFs), which display DNA site recognition specificity with some flexibility built in. TFs, however, are not considered essential to a minimal cellular life. How do they evolve? It has been hypothesized that TFs evolve by gaining specificity (and other functions) on a background of non-specific chromosome structuring proteins. We used the IHF/HU family of DNA binding proteins, in which IHF binds DNA in a sequence-specific manner, whereas HU binds more indiscriminately, to test this hypothesis. We show that HUβ has been present from the bacterial root, while both IHF subunits emerged much later and diversified in Proteobacteria, with HUα having possibly arisen from transfer events in Gammaproteobacteria. By reconstructing ancestral sequences in-silico on a rooted phylogeny of IHF/HU we show that the common ancestor of this family was probably HU-like and therefore non-specific in binding DNA. IHF evolved from a branch of HU after HU had substantially diverged. Various residues characteristic of IHFα and shown to be involved in specific sequence recognition (at least in E. coli) have likely been co-opted from preexisting residues in HU, while those residues of IHFβ have likely evolved independently, suggesting that each of the IHF subunits has undergone different trajectories to acquire their DNA binding properties.

Trace Element Exposure during Pregnancy Has a Persistent Influence on Perinatal Gut Microbiota in Mother-Infant Dyads

Trace elements have been recognized as the modifiers of the gut microbiota. However, population-based evidence about their effects on maternal gut microbiota dynamics, as well as the intergenerational impacts on neonatal gut microbiota, has been lacking. We examined the longitudinal microbiota data from mother-infant dyads and demonstrated that maternal trace element exposure played a pivotal role in shaping the composition and similarity of the mother-infant gut microbiota. Specifically, serum levels of cobalt (Co), molybdenum (Mo), and rubidium (Rb) were identified to cause further fluctuation in the shift of the maternal gut microbiota. Antibiotic usage shortly before or on the delivery day, as well as maternal zinc (Zn) exposure, affected the gut microbiota similarity within mother-infant dyads. Rb demonstrated an intergenerational effect on meconium Bifidobacterium abundance by altering its abundance in the maternal gut. Notably, this effect was strengthened in the vaginal delivery group without antibiotic usage, while it was attenuated in the c-section delivery group. Our results suggest that maternal trace element exposure has a persistent influence on perinatal gut microbiota, which offers novel insights into promoting mother and infant health.

MIP-Chip: Integrated Microfluidic Plasma Separation and Redox-Enhanced Molecularly Imprinted Polymer Succinate Sensor for Whole Blood Metabolite Analysis

The precise quantification of metabolites in bodily fluids is essential for advancing digital health monitoring and clinical diagnostics. Among these fluids, whole blood stands out as a valuable source of predictive metabolite biomarkers, providing critical insights into disease diagnosis and progression. However, traditional blood testing methods often require expensive instrumentation and specialized training, primarily due to the need for plasma extraction to remove interfering blood cells. This study addresses these limitations by introducing a novel, sensitive, rapid, reagent-free, and cost-effective capillary microfluidic-integrated molecularly imprinted polymer (MIP) sensor (MIP-Chip) designed for metabolite detection in whole blood. The MIP-Chip integrates two key components: (1) a highly efficient plasma separation module capable of extracting plasma from whole blood (∼95% efficiency) without requiring sample pretreatment or external active forces and (2) an electrochemical MIP sensor employing an ultrasensitive electrode with on-electrode Prussian Blue nanoparticles (PB NPs) as embedded redox probes for sensitive and specific metabolite detection in the extracted plasma. Using this platform, we successfully quantified succinate, a critical metabolite, across a wide linear concentration range (50 nM-250 μM) with a limit of detection of 5 nM. The device processed 120 μL of whole blood, delivering 8 μL of plasma, and completed the entire workflow-from sample introduction to biomarker detection within 25 min. The MIP-Chip demonstrated exceptional performance, including self-powered assay automation, high specificity for succinate quantification in whole blood, excellent reproducibility, and long-term stability of the MIP-based sensor. These features establish the MIP-Chip as a powerful analytical platform for point-of-care diagnostics, offering a significant step forward in clinical metabolite detection and digital health monitoring.

SARS-CoV-2 biological clones are genetically heterogeneous and include clade-discordant residues

Defective genomes are part of SARS-CoV-2 quasispecies. High-resolution, ultra-deep sequencing of bulk RNA from viral populations does not distinguish RNA mutations, insertions, and deletions in viable genomes from those in defective genomes. To quantify SARS-CoV-2 infectious variant progeny, virus from four individual plaques (biological clones) of a preparation of isolate USA-WA1/2020, formed on Vero E6 cell monolayers, was subjected to further biological cloning to yield 9 second-generation and 15 third-generation sub-clones. Consensus genomic sequences of the biological clones and sub-clones included an average of 2.8 variations per viable genome, relative to the consensus sequence of the parental USA-WA1/2020 virus. This value is 6.5-fold lower than the estimates for biological clones of other RNA viruses such as bacteriophage Qβ, foot-and-mouth disease virus, or hepatitis C virus in cell culture. The mutant spectrum complexity of the nsp12 (polymerase)- and spike (S)-coding region was unique in the progeny of each of 10 third-generation sub-clones; they shared 2.4% of the total of 164 different mutations and deletions scored in the 3,719 genomic residues that were screened. The presence of minority out-of-frame deletions revealed the ease of defective genome production from an individual infectious genome. Several low-frequency point mutations and deletions were clade-discordant in that they were not typical of USA-WA1/2020 but served to define the consensus sequences of future SARS-CoV-2 clades. Implications for SARS-CoV-2 adaptability and COVID-19 control of the viable genome heterogeneity and the generation of complex mutant spectra from individual genomes are discussed.IMPORTANCESequencing of biological clones is a means to identify mutations, insertions, and deletions located in viable genomes. This distinction is particularly important for viral populations, such as those of SARS-CoV-2, that contain large proportions of defective genomes. By sequencing biological clones and sub-clones, we quantified the heterogeneity of the viable complement of USA-WA1/2020 to be lower than exhibited by other RNA viruses. This difference may be due to a reduced mutation rate or to limited tolerance of the large coronavirus genome to incorporate mutations and deletions and remain functional or a combination of both influences. The presence of clade-discordant residues in the progeny of individual biological sub-clones suggests limitations in the occupation of sequence space by SARS-CoV-2. However, the complex and unique mutant spectra that are rapidly generated from individual genomes suggest an aptness to confront selective constraints.

Methodology for microbiome data analysis: An overview

It is known that microbiome and health are related, in addition, recent research has found that microbiome has potential clinical uses. These facts highlight the importance of the microbiome in actual science. However, microbiome data has some characteristics that makes its statistical study challenging. In recent years, longitudinal and non-longitudinal methods have been designed to analyze the microbiota and knowing more about the bacterial behavior. In this article in the form of a review we summarize the characteristics of microbiome data and the statistical methods most widespread to analyze it. We have taken into account if the strategies are longitudinal or not. We also classify the methods based on their specific analytical objectives and based on their mathematical characteristics. The methods are structured according to their biological goals and mathematical features, ensuring that the insights provided are both relevant and accessible to professionals in biology and statistics. We present this review as a reference for the most widely used methods in microbiome data analysis and as a foundation for identifying potential areas for future research. We want to point out that this review can be particularly useful to remark the importance of the methodology designed in order to study microbiome longitudinal datasets.

Bacterial symbiont as game changers for Aphis craccivora Koch's fitness and survival across distinct climate types

Symbiotic bacteria play a crucial role in the survival, development, and adaptation of aphids to environmental conditions. Buchnera aphidicola (Enterobacterales: Erwiniaceae), the obligate endosymbiont of aphids, is essential for their fitness, while facultative symbionts may provide additional ecological advantages under specific conditions. A comprehensive understanding of how these symbiotic relationships respond to different climatic environments is essential for assessing aphid adaptability and potential implications for biological control. The present study investigates the vital interactions between the obligate bacterial endosymbiont, Buchnera aphidicola, and four facultative bacterial endosymbionts (Arsenophonus sp., Hamiltonella defensa, Serratia symbiotica, and Regiella insecticola), in black cowpea aphid (BCA), in the context of different climate conditions. The BCA specimens were obtained from the leaves of the host plant, alfalfa, cultivated in three distinct climates: cold semi-arid, hot desert, and humid subtropical climates. The findings, as anticipated, indicated a pervasive prevalence of B. aphidicola in BCAs infesting alfalfa crops across all three climate types. In contrast, the BCAs of each climate type exhibited a distinct array of facultative symbionts. The highest number of facultative endosymbionts was exhibited by BCAs from the humid subtropical climate, followed by BCAs from the cold semi-arid climate, whereas none of them were detected in BCAs from the hot desert climate. Rigiella insecticola was not detected molecularly in any of the BCAs from the three climates. Following the eradication of the obligate symbiont Buchnera aphidicola by the antibiotic rifampicin in BCAs, the effects on three categories of parameters were assessed, including life cycle stages, reproductive traits, and external morphological characteristics of adults. The most significant adverse effects were observed in BCAs inhabiting hot desert followed by those inhabiting cold semi-arid climate; detrimental effects in BCAs of the humid subtropical climate were considerably less pronounced. The observed discrepancies in the parameters of BCAs from the humid subtropical climate can be attributed to the presence of a greater number of facultative symbionts, especially the presence of Serratia symbiotica (Enterobacterales: Yersiniaceae). Following the eradication of B. aphidicola, this facultative symbiont continues to complement the functions of B. aphidicola in the host's survival. Conversely, the low presence of facultative symbionts in cold semi-arid climate or even their absence in hot desert climate exacerbates the negative effects of obligate symbiont eradication. These findings highlight the crucial role of symbionts in aphid biology across a spectrum of climatic conditions, and suggest that shifts in symbiotic relationships may modulate aphid fitness, which could have implications for biological control programs.

ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation in Sipha maydis

Most arthropods live in close association with bacteria. The genomes of associated partners have co-evolved, creating situations of interdependence that are complex to decipher despite the availability of their complete sequences. We developed ArtSymbioCyc, a metabolism-oriented database collection gathering genomic resources for arthropods and their associated bacteria. ArtSymbioCyc uses the powerful tools of the BioCyc community to produce high-quality annotations and to analyze and compare metabolic networks on a genome-wide scale. We used ArtSymbioCyc to study the case of the tripartite symbiosis of the cereal aphid Sipha maydis focusing on amino acid and vitamin metabolisms, as these compounds are known to be important in this strictly phloemophagous insect. We showed that the metabolic pathways of the insect host and its two obligate bacterial associates are interdependent and specialized in the exploitation of Poaceae phloem, particularly for the biosynthesis of sulfur-containing amino acids and most vitamins. This demonstrates that ArtSymbioCyc does not only reveal the individual metabolic capacities of each partner and their respective contributions to the holobiont they constitute but also allows to predict the essential inputs that must come from host nutrition.IMPORTANCEThe evolution has driven the emergence of complex arthropod-microbe symbiotic systems, whose metabolic integration is difficult to unravel. With its user-friendly interface, ArtSymbioCyc (https://artsymbiocyc.cycadsys.org) eases and speeds up the analysis of metabolic networks by enabling precise inference of compound exchanges between associated partners and helps unveil the adaptive potential of arthropods in contexts such as conservation or agricultural control.

Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size-currently exceeding 1012 nucleotides-and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

IMPORTANCE

Accurately identifying the diverse microbes present in a sample, whether from the human gut, a soil sample, or a crime scene, is crucial for fields ranging from medicine to environmental science. Researchers rely on comprehensive DNA databases to match sequenced DNA fragments to known microbial species. However, the widely used NCBI nt database, while vast, poses significant challenges. Its massive size makes it difficult for many researchers to use effectively with taxonomic classifiers, and inconsistencies and contamination within the database can impact the accuracy of microbial identification. This work addresses these challenges by providing cleaned, updated, and validated nt-based databases specifically optimized for the widely used Centrifuge classification tool. This new resource demonstrably reduces errors and improves the reliability of microbial identification across diverse taxonomic groups. Moreover, by providing readily usable indexes, we overcome the size barrier, enabling researchers to leverage the full potential of the nt database for metagenomic analysis. Our findings underscore the need to treat reference databases as dynamic entities, emphasizing continuous quality control and versioning as essential practices for robust and reproducible metagenomics research.

The synthesis of nitric oxide regulated by JNK pathway in the pea aphid to defend against bacterial infection

Compared to other insects, the pea aphid Acyrthosiphon pisum exhibits limited immune responses, particularly due to the absence of many immune genes, including those encoding antimicrobial peptides and key components of the IMD pathway. Prior studies proved that the conserved signaling, Jun N-terminal kinase (JNK) pathway, plays a critical role in the immune system of the pea aphid, and nitric oxide synthase (NOS) is required for the pea aphid's defense against infections. Herein, using in vitro biochemical assays and in vivo bioassays, we demonstrated that the JNK pathway directly regulates the expression of NOS and that the JNK pathway-NOS-NO signal axis is efficient in defending against bacterial infections. The Toll pathway is instrumental for combating bacterial infections, and NO can activate the Toll pathway. The Toll pathway induced by NO regulates the expressions of ROS metabolism, lysosome, and phagocytosis-related genes. NO was identified as a crucial signaling molecule that facilitates communication between the JNK and Toll pathways.

The evolution of robustness and fragility during long-term bacterial adaptation

Theory predicts that well-adapted populations may evolve mechanisms to counteract the inevitable influx of deleterious mutations. While mutational robustness can be directly selected in the laboratory, evidence for its spontaneous evolution during general adaptation is mixed. Moreover, whether robustness evolves to include pleiotropic effects remains largely unexplored. Here, we studied the effects of point mutations in the RNA polymerase of Escherichia coli over a 15,000-generation adaptive trajectory. Fitness effects of both beneficial and deleterious mutations were attenuated in fitter backgrounds. In contrast, pleiotropic effects became more severe and widespread with greater adaptation. These results show that trade-offs between robustness and fragility can evolve in regulatory networks, regardless of whether driven by adaptive or nonadaptive processes. More broadly, they illustrate how adaptation can generate hidden variability, with unpredictable evolutionary consequences in new environments.

Construction of a comprehensive library of repeated sequences for the annotation of Citrus genomes

BACKGROUND

The comprehensive annotation of repeated sequences in genomes is an essential prerequisite for studying the dynamics of these sequences over time and their involvement in gene regulation. Currently, the diversity of repeated sequences in Citrus genomes is only partially characterized because the annotations have been performed using heterogeneous bioinformatics tools, each with its specificity and dedicated only to the annotation of transposable elements.

RESULTS

We combined complementary repeat-finding programs including REPET, CAULIFINDER, and TAREAN, to enable the identification of all types of repetitive sequences found in plant genomes, including transposable elements, endogenous caulimovirids, and satellite DNAs. A fine-grained annotation method was first developed to create a consensus sequence library of repeated sequences identified in the genome assemblies of C. medica, C. micrantha, C. reticulata, and C. maxima, the four ancestral parental species involved in the formation of economically valuable cultivated Citrus varieties. A second, faster annotation method was developed to enrich the dataset by adding new repeated sequences retrieved from genome assemblies of other Citrus species and closely related species belonging to the Aurantioideae subfamily. The final reference library contains 3,091 consensus sequences, of which 94.5% are transposable elements. The diversity of endogenous caulimovirids was characterized for the first time within the genus Citrus, contributing 160 consensus sequences to the final reference library. Finally, 10 satellite DNAs were also identified.

CONCLUSION

Combining multiple repeat detection methods enables the comprehensive annotation of all repeated sequences in Citrus genomes. Using the final reference library reported in this work will improve our understanding of the dynamics of repeated sequences during Citrus speciation, particularly following the genome duplication and hybridization events that led to modern cultivars. The exploration of repeat position insertions along chromosomes using the developed web interface, RepeatLoc Citrus, will also make it possible to further investigate the role of transposable elements and endogenous caulimovirids in genome structure and gene regulation in Citrus species.

Multiple stressors affect function rather than taxonomic structure of freshwater microbial communities

Microbial community responses to environmental stressors are often characterised by assessing changes in taxonomic structure, but such changes, or lack thereof, may not reflect functional changes that are critical to ecosystem processes. We investigated the individual and combined effects of nutrient enrichment ( + 10 mg/L N, + 1 mg/L P) and salinisation ( + 15 g/L NaCl)-key stressors in freshwater systems-on the taxonomic structure and metabolic function of benthic microbial communities using 1000 L open freshwater ponds established >10 years ago in the field. Combined stressors drove strong decreases in maximum and mean total carbon metabolic rates and shifted carbon metabolic profiles compared to either stressor individually and compared to ambient conditions. These metabolic functional changes did not recover through time and occurred without significant alterations in bacterial community taxonomic structure. These results imply that critical functions, including organic carbon release, are likely to be impaired under multiple stressors, even when taxonomic structure remains stable.

Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications

Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.

The lotus seed starch-EGCG complex modulates obesity in C57BL/6J mice through the regulation of the gut microbiota

The starch-polyphenol complex, identified as RS5-resistant starch, has been shown to regulate the gut environment and inhibit metabolic diseases, including obesity. In a study with C57BL/6 obese mice fed LSE, potential anti-obesity effects were demonstrated through physiological and biochemical assessments, gut microbiota analysis, and mechanistic insights. The study showed that LSE reduced mice body weight, serum total cholesterol, and triglycerides (P < 0.05). Serum inflammatory markers (TNF-α, IL-6, IL-1β) and LPS levels were significantly decreased, while glucose tolerance (AUC reduced by 29.29 %) and insulin sensitivity (AUC reduced by 31.79 %) were improved. Histological analysis indicated reduction in adipocyte size and attenuation of hepatic steatosis. Gut microbiota profiling demonstrated LSE increased beneficial bacteria genera Faecalibacterium, Bifidobacterium, and Akkermansia. This correlated with enhanced SCFA production (acetate 41.53 %, propionate 45.52 %, butyrate 57.49 % increase). These findings demonstrate that LSE exerts anti-obesity effects through modulation of the gut microbiota-SCFA-metabolic axis, supporting starch-polyphenol complexes as functional food candidates.