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Background Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied. Methods A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis. Results K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae -infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations. Conclusions The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier. [ABSTRACT FROM AUTHOR]

Dysbiosis within microbiomes has been increasingly implicated in many systemic illnesses, such as cardiovascular disease, metabolic syndrome, respiratory infections, and Alzheimer disease (Ad). The correlation between Ad and microbial dysbiosis has been repeatedly shown, yet the etiologic cause of microbial dysbiosis remains elusive. From a neuropathology perspective, abnormal (often age-related) changes in the brain, associated structures, and bodily lumens tend toward an accumulation of oxygen-depleted pathologic structures, which are anaerobically selective niches. These anaerobic environments may promote progressive change in the microbial community proximal to the brain and thus deserve further investigation. In this review, we identify and explore what is known about the anaerobic niche near or associated with the brain and the anaerobes that it is harbors. We identify the anaerobe stakeholders within microbiome communities and the impacts on the neurodegenerative processes associated with Ad. Chronic oral dysbiosis in anaerobic dental pockets and the composition of the gut microbiota from fecal stool are the 2 largest anaerobic niche sources of bacterial transference to the brain. At the blood-brain barrier, cerebral atherosclerotic plaques are predominated by anaerobic species intimately associated with the brain vasculature. Focal cerebritis/brain abscess and corpora amylacea may also establish chronic anaerobic niches in direct proximity to brain parenchyma. In exploring the anaerobic niche proximal to the brain, we identify research opportunities to explore potential sources of microbial dysbiosis associated with Ad. [ABSTRACT FROM AUTHOR]

Summary: Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression.To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full‐bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings.Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression.The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression. [ABSTRACT FROM AUTHOR]

Posttraumatic stress disorder (PTSD) is a common consequence of traumatic injury, yet certain biological factors contributing to PTSD are poorly understood. The gut microbiome may influence mental health outcomes, but its role in heterogeneous PTSD presentations requires elucidation. Bacterial composition was examined in adults 2–4 years post-trauma with probable PTSD (n = 24) versus trauma-exposed controls without probable PTSD (n = 24). 16S rRNA sequencing and bioinformatic tools assessed microbial diversity and abundance. Relationships between taxa and PTSD symptom clusters were evaluated. No differences were found in overall microbial community structure between groups. The probable PTSD group exhibited significantly reduced Actinobacteriota and increased Verrucomicrobiota phylum abundance compared to controls. Specific taxa showed notable inverse associations with negative mood/cognition versus hyperarousal symptoms. Prevotella and Ruminococcaceae were negatively associated with negative mood but positively associated with hyperarousal. Results demonstrate microbial signatures of probable PTSD subtypes, highlighting the microbiome as a potential mediator of heterogeneous trauma psychopathology. Definition of PTSD microbial correlates provides a foundation for personalized psychobiotic interventions targeting predominant symptom profiles. • PTSD group had lower relative Actinobacteriota, higher Verrucomicrobiota compared to controls. • No differences in overall community structure, diversity, or other major phyla • Prevotella, Ruminococcaceae, Lachnospiraceae inversely related to symptom clusters. • Findings suggest microbial heterogeneity across PTSD subtypes. [ABSTRACT FROM AUTHOR]

Polygonum cuspidatum, alternatively known as Fallopia japonica or Reynoutria japonica, is a perennial herb belonging to the Polygonaceae family. Commonly called Japanese knotweed or Asian knotweed, this plant is native to East Asia, particularly in regions such as Korea, China, and Japan. It has successfully adapted to a wide range of habitats, resulting in it being listed as a pest and invasive species in several countries in North America and Europe. This study focuses on analysing the composition of the bacterial and fungal endophytic communities associated with Japanese knotweed growing in the Russian Far East, employing next-generation sequencing (NGS) and a cultivation-based method (microbiological sowing). The NGS analysis showed that the dominant classes of endophytic bacteria were Alphaproteobacteria (28%) and Gammaproteobacteria (28%), Actinobacteria (20%), Bacteroidia (15%), and Bacilli (4%), and fungal classes were Agaricomycetes (40%), Dothideomycetes (24%), Leotiomycetes (10%), Tremellomycetes (9%), Pezizomycetes (5%), Sordariomycetes (3%), and Exobasidiomycetes (3%). The most common genera of endophytic bacteria were Burkholderia-Caballeronia-Parabukholderia, Sphingomonas, Hydrotalea, Methylobacterium-Metylorubrum, Cutibacterium, and Comamonadaceae, and genera of fungal endophytes were Marasmius, Tuber, Microcyclosporella, Schizothyrium, Alternaria, Parastagonospora, Vishniacozyma, and Cladosporium. The present data showed that the roots, leaves, and stems of P. cuspidatum have a greater number and diversity of endophytic bacteria and fungi compared to the flowers and seeds. Thus, the biodiversity of endophytic bacteria and fungi of P. cuspidatum was described and analysed for the first time in this study. [ABSTRACT FROM AUTHOR]

The gastrointestinal (GI) microbiome of chelonians (testudines) plays an important role in their metabolism, nutrition, and overall health but the GI microbiome of three-toed box turtles (Terrapene carolina triunguis) has yet to be characterized. How the GI microbiome responds to rapidly rising environmental temperatures has also not been studied extensively in ectotherms, specifically chelonians. In this study, twenty (20) T.c.triunguis were split into control and experimental groups. The experimental group experienced 4.5°C increases every two weeks while the control group stayed at a constant ambient temperature (24°C) through the entirety of the experiment. Before each temperature increase, all turtles had cloacal swab samples taken. These samples underwent DNA extraction followed by 16S rRNA gene sequencing and microbial community analyses. Differences in diversity at the community level in the controls compared to the experimental groups were not statistically significant, indicating microbiome resilience to rapid temperature changes in T.c.triunguis, although some differentially abundant lineages were identified. Interestingly, an amplicon sequence variant belonging to the Erysipelothrix spp. was exclusively enriched in the highest temperature group relative to controls. Overall, our work suggests that there may be an innate robustness to rapid temperature swings in the microbiome of T.c.triunguis which are native to temperate North America. Despite this resilience, Erysipelothrix spp. was enriched at the highest temperature. Phylogenetic analysis of this amplicon variant showed that it is a close relative of Erysipelothrix rhusiopathiae, a pathogen of zoonotic importance associated with both wildlife and livestock. [ABSTRACT FROM AUTHOR]

Background: Since the consensus of ISAPP on the definition of the term "postbiotic" there has been an enthusiasm for publications in review form—their number being disproportionate to the primary research. The aim of this bibliometry is to analyze the bibliometric trends of this newfound interest in the field. Methods: Search of the PubMed database for review articles on postbiotics, published between November 2021 and June 2024. Results: Analysis was performed on 92 review articles, the number corresponding to 2.9 reviews per month. China, Poland, Italy, Iran and India had the maximum productivity among the 32 countries involved; 21 articles were published in 13 journals with the highest impact factor, while 45 were in 16 journals with an IF between 4.0 and 4.9. The authors were mainly affiliated to universities with specialization in both basic research and technology, as well as food science. The top five publications regarding the citations received, published in Foods (2), EBioMedicine, Biomolecules, and Front. Nutr., have collected between 138 and 109 citations. Conclusions: The ever-growing number of reviews regarding postbiotics is perhaps disproportionate to the actual original research in the field. Further clinical trials would extend and deepen the subject and facilitate the drowning of more robust conclusions in relation to their effects. [ABSTRACT FROM AUTHOR]

Background: The human microbiome, comprising trillions of microorganisms, significantly influences human health and disease. During critical periods like the perinatal phase, the microbiome undergoes significant changes, impacting lifelong health. Tobacco smoke, a known environmental pollutant, has adverse effects on health, particularly during pregnancy. Despite this, its association with the perinatal microbiome remains understudied. Methods: We conducted a systematic review to integrate findings on perinatal tobacco smoke exposure and its association with the maternal and neonatal microbiomes. We conducted a comprehensive literature search in the PubMed, Scopus, and Web of Science databases from January 2000 to February 2024. We selected studies that met predefined inclusion criteria and performed data extraction. Results: The review included eight studies that revealed diverse associations of perinatal tobacco exposure with the maternal and neonatal microbiome. Active smoking during pregnancy was linked to alterations in microbiome composition and diversity in children. Maternal smoking correlated with increased Firmicutes abundance and decreased Akkermansia muciniphila abundance in offspring. Additionally, exposure to thirdhand smoke in neonatal intensive care units was related to infant microbiome diversity. Infants exposed to tobacco smoke showed various microbial changes, suggesting potential implications for childhood health outcomes, including obesity risk. Conclusions: Perinatal exposure to tobacco smoke exerts significant influence on the maternal and neonatal microbiomes, with potential implications for long-term health outcomes. Addressing socioeconomic and psychological barriers to smoking cessation, implementing stricter smoking regulations, and promoting public health campaigns are essential steps towards reducing tobacco-related harm during the perinatal period. Further longitudinal studies and standardized assessment methods are needed to validate these findings and guide the development of effective preventive measures. [ABSTRACT FROM AUTHOR]

Metformin is the most commonly prescribed medication for treating type 2 diabetes (T2D). It is known that metformin can alter the gut microbiome, which influences the effectiveness of metformin treatment. We posited that if the gut microbiome, a reservoir of the resistome, is altered, then the resistome should change as well. To test this hypothesis, we reanalyzed microbiome data generated by Wu et al. (Nat Med 23(7):850–858, 2017), identifying antibiotic resistance genes (ARGs) and bacterial species. Through read-based analysis, we observed that the abundance of ARGs indeed changed in many samples treated with metformin. Moreover, the altered pattern was sufficiently heterogeneous across individual samples to allow subcategorization. We also found a strong correlation between the abundance of multidrug-resistant ARGs (MDR-ARGs) and the presence of E. coli. The contig-based analysis led to the same conclusion: an increase in MDR-ARGs due to metformin was associated with an increase in E. coli. In relation to this, we were able to confirm that the majority of MDR-ARGs are likely to originate from E. coli. These results suggest that metformin may have the potential side effect of increasing E. coli carrying ARGs, particularly MDR-ARGs, which could be a concern in T2D therapy that relies on metformin. [ABSTRACT FROM AUTHOR]

Objective Methods Results Conclusion Bacterial vaginosis (BV) is a common inflammatory condition affecting the vaginal microbiome. In the present study we aimed to explore the relationship between dietary inflammatory index, plant‐based dietary index, and BV.In this case–control study, 143 individuals with BV and 151 healthy participants aged 15–45 years were included. Bacterial vaginosis diagnosis was based on the Amsel criteria by a gynecologist. Participants' dietary intakes over the past year were assessed using a 168‐item food frequency questionnaire. Logistic regression models were employed to analyze the association between dietary inflammatory index, plant‐based dietary index, and BV odds.Our study revealed that elevated dietary inflammatory index scores were strongly associated with higher BV odds in the crude model (odds ratio [OR]: 2.88, 95% confidence interval [CI]: 1.57–5.30, P value <0.001), and even after accounting for potential confounding factors (adjusted OR: 3.52, 95% CI: 1.66–7.46, P value = 0.001). While no significant relationship was observed between total plant‐based dietary index and healthy plant‐based dietary index scores with BV odds, a clear positive association existed between unhealthy plant‐based dietary index and the odds of BV (aOR: 2.13, 95% CI: 1.09–4.15, P value = 0.018).A positive correlation may exist between unhealthy plant‐based dietary index and the likelihood of BV. Furthermore, the dietary inflammatory index may remain linked to increased BV odds. [ABSTRACT FROM AUTHOR]

Understanding the environmental drivers of microbial H 2 metabolisms is crucial for evaluating the risks for geological hydrogen storage. This study investigates how mineralogy and temperature affect H 2 consumption kinetics and metabolic activity of a microbial consortium containing methanogens, homoacetogens and sulfate reducers, incubated at 25, 34 and 40 °C under H 2 /CO 2 (80/20, v/v; 2 bars) with different rock powders (basalt, calcite, gypsum, and sandstone). The presence of gypsum favors sulfate reduction over methanogenesis and homoacetogenesis, especially at 25 °C. Methanogenesis is dominant at 34 and 40 °C with all sulfate-free mineralogies. At 25 °C, homoacetogenic bacteria are favored over methanogens and acetate production varies with the mineralogy. This suggests interactions of the microbial community with the rock powders, which may serve as a surface to form biofilms. These metabolic shifts are associated with radical changes in microbial populations, highlighting that ecosystems plasticity towards H 2 also depends on the mineralogical composition of the reservoir. • Both temperature and mineralogy affect H 2 consumption kinetics. • Gypsum powder favors sulfate reduction over methanogenesis and homoacetogenesis. • Low temperature favors homoacetogenesis over methanogenesis. • Proportions of methanogenesis and homoacetogenesis vary with the substrate mineralogy. • Metabolic shifts are associated with radical changes in microbial populations. [ABSTRACT FROM AUTHOR]

The human microbiome is a diverse ecosystem of microorganisms that reside in the body and influence various aspects of health and well-being. Recent advances in sequencing technology have brought to light microbial communities in organs and tissues that were previously considered sterile. The gut microbiota plays an important role in host physiology, including metabolic functions and immune modulation. Disruptions in the balance of the microbiome, known as dysbiosis, have been linked to diseases such as cancer, inflammatory bowel disease and metabolic disorders. In addition, the administration of antibiotics can lead to dysbiosis by disrupting the structure and function of the gut microbial community. Targeting strategies are the key to rebalancing the microbiome and fighting disease, including cancer, through interventions such as probiotics, fecal microbiota transplantation (FMT), and bacteria-based therapies. Future research must focus on understanding the complex interactions between diet, the microbiome and cancer in order to optimize personalized interventions. Multidisciplinary collaborations are essential if we are going to translate microbiome research into clinical practice. This will revolutionize approaches to cancer prevention and treatment. ● Gut microbiome influences cancer treatment efficacy and outcomes. ● Dysbiosis is associated with inflammatory diseases and metabolic disorders. ● Antibiotic-induced dysbiosis challenges human health and microbiome resilience. ● Novel interventions such as probiotics and FMT hold promise for disease management. ● A comprehensive review synthesizes multidisciplinary research on microbiome dynamics. [ABSTRACT FROM AUTHOR]

Background: This study conducts a systematic review through meta-analysis, comparing the composition and diversity of the gut microbiome in patients with esophageal cancer and healthy individuals, and explores the relationship between risk factors and related factors of esophageal cancer. Methods: According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA), we comprehensively searched the databases of PubMed, Web of Science, Embase, Cochrane Library. In addition, we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis. We also implemented the Newcastle-Ottawa Scale (NOS), funnel plot analysis, Egger’s test, and Begg’s test to assess the risk of bias. Results: In this study, a total of 328 studies were identified through the literature search. Among them, 117 duplicate studies were removed, and 202 studies were excluded based on inclusion and exclusion criteria. Finally, 9 studies were included in the analysis, involving a total of 216 patients with esophageal carcinoma and 352 healthy controls. Four studies provided Chao1 index for quantitative consolidation (ES = 637.41, 95% CI: 549.16 to 725.66, p = 0.000, I² = 98.2%). Two studies [27, 29] reported ACE index (ES = 438.89, 95% CI: 362.42 to 515.35, p = 0.000, I² = 97%). Seven studies [26,27,29,30,32] reported the Shannon index for quantitative consolidation (ES = 4.38, 95% CI: 3.95 to 4.81, p = 0.000, I 2 = 99%). At the phylum level, the abundance of Bacteroidetes(ES = 37.8, 95% CI: 25.75 to 49.85, p = 0.000, I² = 87.2%) and Proteobacteria(ES = 7.48, 95% CI: 5.02 to 8.85, p = 0.04, I² = 2.4%) have statistical difference between ESCC and HC. There was no significant difference between ESCC and HC in the abundance of genera(p>0.05). Conclusions: This observational meta-analysis revealed that changes in the GM were correlated with esophageal carcinoma, and variations in some advantageous GM might involve regional differences. Additionally, the study aims to facilitate early diagnosis of esophageal cancer and improve screening and diagnostic efficiency [ABSTRACT FROM AUTHOR]

Opioid drugs have been long known to induce different responses in males compared to females, however, the molecular mechanisms underlying these effects are yet to be fully characterized. Recent studies have established a link between the gut microbiome and behavioral responses to opioids. Chronic opioid use is associated with gut dysbiosis, or microbiome disruptions, which is thought to contribute to altered opioid analgesia and reward processing. Gut microbiome composition and functioning have also been demonstrated to be influenced by sex hormones. Despite this, there is currently very little work investigating whether sex differences in the gut microbiome mediate sexdependent responses to opioids, highlighting a critical gap in the literature. Here, we briefly review the supporting evidence implicating a potential role for the gut microbiome in regulating sexually dimorphic opioid response and identify areas for future research. [ABSTRACT FROM AUTHOR]

Introduction: Soybean is a significant export product for several countries, including the United States and Brazil. There are numerous varieties of soybean. Among them, a genetically modified type known as INTACTA RR2 PRO™ has been designed to demonstrate resistance to glyphosate and to produce toxins that are lethal to several species of caterpillars. Limited information is available on the use of Trichoderma harzianum and Bacillus subtilis to promote plant growth and their impact on the plant microbiome. Methods: This study aimed to evaluate the effects of these microorganisms on this soybean cultivar by analyzing parameters, such as root and shoot dry matter, nutritional status, and root and soil microbial diversity. Results: The results indicated that treatments with B. subtilis alone or in combination with T. harzianum as seed or seed and soil applications significantly enhanced plant height and biomass compared to the other treatments and the control. No significant differences in phosphorus and nitrogen concentrations were detected across treatments, although some treatments showed close correlations with these nutrients. Microbial inoculations slightly influenced the soil and root microbiomes, with significant beta diversity differences between soil and root environments, but had a limited overall impact on community composition. Discussion: The combined application of B. subtilis and T. harzianum particularly enhanced plant growth and promoted plant-associated microbial groups, such as Rhizobiaceae, optimizing plant-microbe interactions. Furthermore, the treatments resulted in a slight reduction in fungal richness and diversity. [ABSTRACT FROM AUTHOR]

Background: The commercialization of space travel will soon lead to many more people living and working in unique built environments similar to the International Space Station, which is a specialized closed environment that contains its own indoor microbiome. Unintended microbial growth can occur in these environments as in buildings on Earth from elevated moisture, such as from a temporary ventilation system failure. This growth can drive negative health outcomes and degrade building materials. We need a predictive approach for modeling microbial growth in these critical indoor spaces. Results: Here, we demonstrate that even short exposures to varying elevated relative humidity can facilitate rapid microbial growth and microbial community composition changes in dust from spacecraft. We modeled fungal growth in dust from the International Space Station using the time-of-wetness framework with activation and deactivation limited growth occurring at 85% and 100% relative humidity, respectively. Fungal concentrations ranged from an average of 4.4 × 106 spore equivalents per milligram of dust in original dust with no exposure to relative humidity to up to 2.1 × 1010 when exposed to 100% relative humidity for 2 weeks. As relative humidity and time-elevated increased, fungal diversity was significantly reduced for both alpha (Q < 0.05) and beta (R2 = 0.307, P = 0.001) diversity metrics. Bacteria were unable to be modeled using the time-of-wetness framework. However, bacterial communities did change based on constant relative humidity incubations for both beta (R2 = 0.22, P = 0.001) and alpha diversity decreasing with increasing moisture starting at 85% relative humidity (Q < 0.05). Conclusion: Our results demonstrate that moisture conditions can be used to develop and predict changes in fungal growth and composition onboard human-occupied spacecraft. This predictive model can be expanded upon to include other spacecraft environmental factors such as microgravity, elevated carbon dioxide conditions, and radiation exposure. Understanding microbial growth in spacecraft can help better protect astronaut health, fortify spacecraft integrity, and promote planetary protection as human activity increases in low-Earth orbit, the moon, Mars, and beyond. 5L5VMn4841emXVRzhjbC6H Video Abstract [ABSTRACT FROM AUTHOR]

Soil microbial mutualists like rhizobia bacteria can promote the establishment of rare, late‐successional legumes. Despite restoration efforts, these mutualists are often absent in the microbiome. Therefore, restoring this mutualism by directly inoculating rare legumes with rhizobia mutualists may increase plant establishment. We inoculated seedlings of Amorpha canescens, Dalea purpurea, and Lespedeza capitata with three strains of species‐specific rhizobia each to investigate how this mutualism would promote growth in the field and in the greenhouse. Because many herbaceous plants are vulnerable to herbivory, we used exclosures for half of our field transplantations to prevent mammalian herbivory. We did not find that rhizobia bacteria directly promoted the growth of our legumes in the field but rather that herbivory and environmental conditions overwhelmed the effects of the rhizobia. Of the plants transplanted, only 17.78% of 180 survived to the end of the growing season, all of which were protected from herbivory. Survival at the end of the growing season was also greater in the northern, drier end of the field site. In the second growing season, plants were more likely to survive in the exclosure treatment, while only four recovered in the open treatment. In the greenhouse, we found increased nodulation with inoculations, supporting the hypothesis that species‐specific mutualists are absent from restoration sites. Though several recent studies have shown that restoring mutualistic interactions has the potential to dramatically improve the outcomes of ecological restoration, our results show that protecting rare species from herbivory after transplantation might achieve greater gains in establishment. [ABSTRACT FROM AUTHOR]

This study aimed to compare the gut and oral microbiota composition of professional male football players and amateurs. Environmental and behavioral factors are well known to modulate intestinal microbiota composition. Active lifestyle behaviors are involved in the improvement of metabolic and inflammatory parameters. Exercise promotes adaptational changes in human metabolic capacities affecting microbial homeostasis. Twenty professional football players and twelve amateurs were invited to the study groups. Fecal and oral microbiota were analyzed using next-generation sequencing of the 16S rRNA gene. Diversity in the oral microbiota composition was similar in amateurs and professionals, while the increase in training intensity reduced the number of bacterial species. In contrast, the analysis of the intestinal microbiota showed the greatest differentiation between professional football players and amateurs, especially during intensive training. Firmicutes were characterized by the largest population in all the studied groups. Intensive physical activity increases the abundance of butyrate and succinate-producing bacteria affecting host metabolic homeostasis, suggesting a very beneficial role for the host immune system's microbiome homeostasis and providing a proper function of the host immune system. [ABSTRACT FROM AUTHOR]

Co‐occurrence networks offer insights into the complexity of microbial interactions, particularly in highly diverse environments where direct observation is challenging. However, identifying the scale at which local and non‐local processes structure co‐occurrence networks remains challenging because it requires simultaneously analyzing network structure within and between local networks. In this context, the rumen microbiome is an excellent model system because each cow contains a physically confined microbial community, which is imperative for the host's livelihood and productivity. Employing the rumen microbiome of 1012 cows across seven European farms as our model system, we constructed and analyzed farm‐level co‐occurrence networks to reveal underlying microbial interaction patterns. Within each farm, microbes tended to close triangles but some microbial families were over‐represented while others under‐represented in these local interactions. Using stochastic block modeling we detected a group structure that reflected functional equivalence in co‐occurrence. Knowing the group composition in one farm provided significantly more information on the grouping in another farm than expected. Moreover, microbes strongly conserved co‐occurrence patterns across farms (also adjusted for phylogeny). We developed a meta‐co‐occurrence multilayer approach, which links farm‐level networks, to test scale signatures simultaneously at the farm and inter‐farm levels. Consistent with the comparison between groups, the multilayer network was not partitioned into clusters. This result was consistent even when artificially disconnecting farm‐level networks. Our results show a prominent signal of processes operating across farms to generate a non‐random, similar (yet not identical) co‐occurrence patterns. Comprehending the processes underlying rumen microbiome assembly can aid in developing strategies for its manipulation. More broadly, our results provide new evidence for the scale at which forces shape microbe co‐occurrence. Finally, the hypotheses‐based approach and methods we developed can be adopted in other systems to detect scale signatures in species interactions. [ABSTRACT FROM AUTHOR]

Background: Inulin and inulin-derived fructooligosaccharides (FOS) are well-known prebiotics for use in companion animals and livestock. The mechanisms by which FOS contribute to health has not been fully established. Further, the fine chemistry of fructan structures from diverse sources, such as graminan-type fructans found in cereal crops, has not been fully elucidated. New methods to study fructan structure and microbial responses to these complex carbohydrates will be key for evaluating the prebiotic potency of cereal fructans found in cattle feeds. As the rumen microbiome composition is closely associated with their metabolic traits, such as feed utilization and waste production, prebiotics and probiotics represent promising additives to shift the microbial community toward a more productive state. Results: Within this study, inulin, levan, and graminan-type fructans from winter wheat, spring wheat, and barley were used to assess the capacity of rumen-derived Bifidobacterium boum, Bifidobacterium merycicum, and Lactobacillus vitulinus to metabolize diverse fructans. Graminan-type fructans were purified and structurally characterized from the stems and kernels of each plant. All three bacterial species grew on FOS, inulin, and cereal crop fructans in pure cultures. L. vitulinus was the only species that could metabolize levan, albeit its growth was delayed. Fluorescently labelled polysaccharides (FLAPS) were used to demonstrate interactions with Gram-positive bacteria and confirm fructan metabolism at the single-cell level; these results were in agreement with the individual growth profiles of each species. The prebiotic potential of inulin was further investigated within naïve rumen microbial communities, where increased relative abundance of Bifidobacterium and Lactobacillus species occurred in a dose-dependent and temporal-related manner. This was supported by in situ analysis of rumen microbiota from cattle fed inulin. FLAPS probe derived from inulin and fluorescent in situ hybridization using taxon-specific probes confirmed that inulin interacts with Bifidobacteria and Lactobacilli at the single-cell level. Conclusion: This research revealed that rumen-derived Bifidobacteria and Lactobacilli vary in their metabolism of structurally diverse fructans, and that inulin has limited prebiotic potential in the rumen. This knowledge establishes new methods for evaluating the prebiotic potential of fructans from diverse plant sources as prebiotic candidates for use in ruminants and other animals. [ABSTRACT FROM AUTHOR]

Introduction: Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods: We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results: Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion: This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera. [ABSTRACT FROM AUTHOR]

Background: Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. Results: Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. Conclusions: Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. 2Spd16sRC6jnqdSe2SRbtQ Video Abstract [ABSTRACT FROM AUTHOR]

Over the past decade, there has been a growing interest in common octopus aquaculture, prompted by several factors such as the increase in market demand, the decline in overall fisheries and the search for more sustainable food resources. Nevertheless, this interest has raised concerns about the potential impact of largescale production and intensified farming practices in the future. This study aims to establish a baseline understanding of the natural microbial communities that inhabit skin mucus of the common octopus, describe its core microbiota, and assess the impact of captive rearing on these communities and animal welfare. The skin microbiome of wild-captured octopuses was compared with that of reared in aquaculture using 16S ribosomal RNA metabarcoding. The findings show that the core microbiota of octopus mucosal skin is dominated by the phyla Bacteroidota and Pseudomonadota, with Aurantivirga, Pseudofulvibacter, and Rubritalea being the most abundant genera. Despite differences in abundance, the microbiota composition and diversity between wild and aquaculture octopuses were similar. Wild samples had an enrichment of Gammaproteobacteria, including potentially pathogenic species such as Vibrio spp., Photobacteriumswingsii, and Lactococcus garvieae, which were less prevalent or absent in aquaculture samples. KEGG functional pathways predictions indicated a higher enrichment in functional pathways related to xenobiotic remediation in wild samples, reflecting their need to adapt to a more variable and potentially contaminated environment. This is the first study to characterize the mucosal skin microbiome of the common octopus and to compare wild and aquaculture specimens. The results suggest that current aquaculture practices support animal welfare through the use of controlled hatchery environments and high-quality water conditions. These insights are valuable for the development of sustainable and responsible aquaculture practices, with the octopus microbiome serving as a potential biomarker for health status and animal welfare. [ABSTRACT FROM AUTHOR]

This document is an editorial published in the journal Frontiers in Microbiology. It discusses a research topic on bacteriocins and other ribosomally synthesized and post-translationally modified peptides (RiPPs) as modulators of the microbiome. The research topic includes seven articles that cover various aspects of these peptides, such as their impact on bacterial populations in the human intestinal microbiota, the regulation of gene transcription, and the characterization of antimicrobial peptides. The studies provide insights into the ability of RiPPs to modulate microbiomes and have potential applications in human and animal health, agriculture, and other fields. This Research Topic consists of several studies on bacteriocins and ribosomally synthesized and post-translationally modified peptides (RiPPs) and their applications in biotechnology and human health. The studies explore the mechanisms of action of specific bacteriocins, optimize the production of bacteriocins through heterologous expression, and investigate the potential of circular bacteriocins and RiPPs in various contexts. One review article focuses on probiotic streptococcal strains that produce bacteriocin-like inhibitory substances (BLIS) and their potential in modulating the oral microbiome. Overall, these studies provide valuable insights into the diverse applications of bacteriocins and RiPPs and will be of interest to researchers and those interested in microbiology. [Extracted from the article]

Metals and their nanoparticles can induce toxicities that influence the survival of both microorganisms and macroorganisms. The current study reports on the impact of heavy metal pollution on the microbiome of estuarine and coastal sediments, where the settling and final remineralization of organic matter occur. Sediment samples collected from the Cochin estuary along the southwest coast of India and its adjacent coast showed high concentrations of cadmium (Cd) and zinc (Zn). The contamination factor (CF), calculated by comparing the concentration of metals in each station with that of shale value for Cd and Zn, ranged from 5.2 to 8.7 and 1.5 to 2.0 respectively, in the estuarine and coastal stations. Microbiome analysis revealed that bacteria were common across all stations but varied in relative abundance. Proteobacteria, Chloroflexi, Actinobacteria, Desulfobacteria, and Acidobacteria were the major bacterial phylum found in all stations. More than 70% of the bacteria were tolerant to 1 mM concentration of Cd. The findings of our study suggest that metal pollution can influence the microbiome of sediments in the estuaries and coasts. Bacteria with metal tolerance may dominate in polluted areas, but their participation in remineralization may be impaired, as evident in our previous reports. This impairment could ultimately influence the dynamics of the food web and the biogeochemical cycling of nutrients, necessitating further research. [ABSTRACT FROM AUTHOR]

Many chronic inflammatory diseases are attributed to disturbances in host-microbe interactions, which drive immune-mediated tissue damage. Depending on the anatomic setting, a chronic inflammatory disease can exert unique local and systemic influences, which provide an exceptional opportunity for understanding disease mechanism and testing therapeutic interventions. The oral cavity is an easily accessible environment that allows for protective interventions aiming at modulating the immune response to control disease processes driven by a breakdown of host-microbe homeostasis. Periodontal disease (PD) is a prevalent condition in which quantitative and qualitative changes of the oral microbiota (dysbiosis) trigger nonresolving chronic inflammation, progressive bone loss, and ultimately tooth loss. Here, we demonstrate the therapeutic benefit of local sustained delivery of the myeloid-recruiting chemokine (C-C motif) ligand 2 (CCL2) in murine ligature-induced PD using clinically relevant models as a preventive, interventional, or reparative therapy. Local delivery of CCL2 into the periodontium inhibited bone loss and accelerated bone gain that could be ascribed to reduced osteoclasts numbers. CCL2 treatment up-regulated M2-macrophage and downregulated proinflammatory and pro-osteoclastic markers. Furthermore, single-cell ribonucleic acid (RNA) sequencing indicated that CCL2 therapy reversed disease-associated transcriptomic profiles of murine gingival macrophages via inhibiting the triggering receptor expressed on myeloid cells-1 (TREM-1) signaling in classically activated macrophages and inducing protein kinase A (PKA) signaling in infiltrating macrophages. Finally, 16S ribosomal ribonucleic acid (rRNA) sequencing showed mitigation of microbial dysbiosis in the periodontium that correlated with a reduction in microbial load in CCL2-treated mice. This study reveals a novel protective effect of CCL2 local delivery in PD as a model for chronic inflammatory diseases caused by a disturbance in host-microbe homeostasis. [ABSTRACT FROM AUTHOR]

Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome‐wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus‐dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β‐catenin signaling. Experiments using in‐house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β‐catenin signaling in a GPR81‐dependent manner to promote ISC‐mediated epithelial proliferation. However, heat‐killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus‐lactate‐GPR81 axis, a key mechanism bridging breed‐driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis. [ABSTRACT FROM AUTHOR]

AbstractStrawberries provide a number of potential health promoting phytonutrients to include phenolics, polyphenols, fiber, micronutrients and vitamins. The objective of this review is to provide a comprehensive summary of recent human studies pertaining to the intake of strawberry and strawberry phytonutrients on human health. A literature search conducted through PubMed and Cochrane databases consolidated studies focusing on the effects of strawberry intake on human health. Articles were reviewed considering pre-determined inclusion and exclusion criteria, including experimental or observational studies that focused on health outcomes, and utilized whole strawberries or freeze-dried strawberry powder (FDSP), published between 2000–2023. Of the 60 articles included in this review, 47 were clinical trials, while 13 were observational studies. A majority of these studies reported on the influence of strawberry intake on cardiometabolic outcomes. Study designs included those examining the influence of strawberry intake during the postprandial period, short-term trials randomized with a control, or a single arm intake period controlling with a low polyphenolic diet or no strawberry intake. A smaller proportion of studies included in this review examined the influence of strawberry intake on additional outcomes of aging including bone and brain health, and cancer risk. Data support that the inclusion of strawberries into the diet can have positive impacts during the postprandial period, with daily intake improving outcomes of lipid metabolism and inflammation in those at increased cardiovascular risk. [ABSTRACT FROM AUTHOR]

Background: Periodontitis results from host-microbe dysbiosis and the resultant dysregulated immunoinflammatory response. Importantly, it closely links to numerous systemic comorbidities, and perplexingly contributes to adverse pregnancy outcomes (APOs). Currently, there are limited studies on the distal consequences of periodontitis via oral-gut axis in pregnant women. This study investigated the integrative microbiome-metabolome profiles through multi-omics approaches in first-trimester pregnant women and explored the translational potentials. Methods: We collected samples of subgingival plaques, saliva, sera and stool from 54 Chinese pregnant women at the first trimester, including 31 maternal periodontitis (Perio) subjects and 23 Non-Perio controls. By integrating 16S rRNA sequencing, untargeted metabolomics and clinical traits, we explored the oral-gut microbial and metabolic connection resulting from periodontitis among early pregnant women. Results: We demonstrated a novel bacterial distinguisher Coprococcus from feces of periodontitis subjects in association with subgingival periodontopathogens, being different from other fecal genera in Lachnospiraceae family. The ratio of fecal Coprococcus to Lachnoclostridium could discriminate between Perio and Non-Perio groups as the ratio of subgingival Porphyromonas to Rothia did. Furthermore, there were differentially abundant fecal metabolic features pivotally enriched in periodontitis subjects like L-urobilin and kynurenic acid. We revealed a periodontitis-oriented integrative network cluster, which was centered with fecal Coprococcus and L-urobilin as well as serum triglyceride. Conclusions: The current findings about the notable influence of periodontitis on fecal microbiota and metabolites in first-trimester pregnant women via oral-gut axis signify the importance and translational implications of preconceptional oral/periodontal healthcare for enhancing maternal wellbeing. [ABSTRACT FROM AUTHOR]

Background: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts. Methods: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT. Results: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R2 = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism. Conclusions: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes. Trial registration: Clinicaltrials.gov NCT02185274. [ABSTRACT FROM AUTHOR]

The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes. [ABSTRACT FROM AUTHOR]

In nature, microbes do not thrive in seclusion but are involved in complex interactions within- and between-microbial kingdoms. Among these, symbiotic associations with mycorrhizal fungi and nitrogen-fixing bacteria are namely known to improve plant health, while providing resources to benefit other microbial members. Yet, it is not clear how these microbial symbionts interact with each other or how they impact the microbiota network architecture. We used an extensive co-occurrence network analysis, including rhizosphere and roots samples from six plant species in a natural desert in AlUla region (Kingdom of Saudi Arabia) and described how these symbionts were structured within the plant microbiota network. We found that the plant species was a significant driver of its microbiota composition and also of the specificity of its interactions in networks at the microbial taxa level. Despite this specificity, a motif was conserved across all networks, i.e., mycorrhizal fungi highly covaried with other mycorrhizal fungi, especially in plant roots—this pattern is known as assortativity. This structural property might reflect their ecological niche preference or their ability to opportunistically colonize roots of plant species considered non symbiotic e.g., H. salicornicum, an Amaranthaceae. Furthermore, these results are consistent with previous findings regarding the architecture of the gut microbiome network, where a high level of assortativity at the level of bacterial and fungal orders was also identified, suggesting the existence of general rules of microbiome assembly. Otherwise, the bacterial symbionts Rhizobiales and Frankiales covaried with other bacterial and fungal members, and were highly structural to the intra- and inter-kingdom networks. Our extensive co-occurrence network analysis of plant microbiota and study of symbiont assortativity, provided further evidence on the importance of bacterial and fungal symbionts in structuring the global plant microbiota network. [ABSTRACT FROM AUTHOR]

Introduction: Gingivitis is a common intraoral disease in patients with chronic kidney disease (CKD), which poses a particular interdisciplinary challenge. We aimed to determine the influence of an intensive oral prophylaxis program (OPP) compared to standard prevention measures on the tongue microbiome of young patients with CKD. Methods: Thirty patients with CKD (mean age 14.2 ± 5.2 years) and generalized gingivitis were included. The effects of the intensive OPP were compared with standard prophylaxis according to statutory health insurance (treatment as usual, TAU) as a control. Tongue swabs were taken from the patients at baseline (t1) and after 3 (t2) and 6 (t3) months. Next-generation sequencing of 16S rDNA genes was used to quantitatively characterize microbial communities. Results: There were no differences in the abundance, richness, or diversity of the observed genera and species between the two study groups at baseline or after 3 or 6 months. Furthermore, no change in predefined gingivitis and oral health bacterial clusters were found. At the phylum level, Firmicutes were decreased after intervention in the TAU group (t2TAU 42.9 ± 7.1 to t3TAU 34.8 ± 4.7 (npairs=14), p=0.003; false discovery rate 0.02). The decrease of Firmicutes was not significant in the OPP group. Conclusions: Despite the intensity of dental prophylaxis and decreasing clinical signs of inflammation and decreasing plaque amount, no clinically relevant changes in the tongue microbiome were observed. Our results confirm the conserved and stable nature of the tongue microbiome, even in children with CKD. [ABSTRACT FROM AUTHOR]

Introduction: Accumulating evidence has supported that gut microbiota and metabolite profiles play indispensable roles in the pathogenesis of colorectal cancer (CRC), which ranks as the third most common cancer and the second leading cause of cancer-related deaths worldwide. However, alterations in tumoral or circulating microbiomes in CRC remain incompletely understood. It has been well-documented that tissue or serum microbiomes with low microbial biomass could be screened by use of 2bRAD sequencing for microbiome (2bRAD-M) at the species resolution. Methods: In order to validate the microbial biomarkers distinguishing CRC and the variations in microorganisms present in serum and tumors, we performed 2bRAD-M to characterize the microbiomes in serum and cancer tissues of CRC patients with and without lymph node or liver metastasis. Results: The composition of dominated microbiota in serum was different from that of tissue samples, while the microbial community composition of tumors was similar to that of the tumor-adjacent tissues. The analysis of α-diversity and β-diversity has revealed notable variations in serum microbiota diversities in CRC patients, particularly those with liver metastasis. Multiple CRC-specific microbial species, such as Moraxella A cinereus, Flavobacterium sp001800905, and Acinetobacter albensis, were identified in serum. Complicated functions and KEGG pathways were also confirmed in CRC according to the metastasis status. Discussion: This study has found significant alterations in the microbial compositions and diversities in CRC and CRC-specific microbial species in both circulation and cancer tissues, which may serve as promising biomarkers for the screening, diagnosis and prognosis prediction of CRC. In particular, CRC-specific bacterial taxa are promising markers, holding transformative potentials in establishing personalized screening and risk stratification, refining much earlier non-invasive diagnostic approaches, and enhancing diagnostic sensitivity. [ABSTRACT FROM AUTHOR]

Background: Bovine genital campylobacteriosis (BGC) is a globally important venereal disease of cattle caused by Campylobacter fetus subspecies venerealis. Diagnosis of BGC is highly challenging due to the lack of accurate diagnostic tests. Methods: To characterise the biomarkers for C. fetus venerealis infection, a total of twelve cycling heifers were selected and categorised as vaccinated (n = 6) with Vibrovax® (Zoetis™) and unvaccinated (n = 6). All heifers were oestrous synchronised with a double dose of prostaglandin (PGF2α) 11 days apart and when in oestrous intravaginally challenged with 2.7 x 109 CFU live C. fetus venerealis. DNA extracted from vaginal mucus samples was screened using a C. fetus qPCR and 16S rRNA was characterised using Illumina sequencing (V5-V8 region). Relative abundances of serum proteins were calculated using sequential window acquisition of all theoretical fragment ion spectra coupled to tandem mass spectrometry (SWATH-MS) for all heifers at three timepoints: pre-challenge, post-challenge and post-recovery. Results: In 16S rRNA sequencing of vaginal mucus, Campylobacter spp. appeared two days following challenge in unvaccinated compared to 14 days in vaccinated animals, consistent with the qPCR results. Increased relative abundances of Firmicutes and Campylobacterota were identified after C. fetus venerealis challenge and were associated with C. fetus venerealis in vaccinated and unvaccinated heifers. Greater relative abundance of Streptococcus spp. was observed during oestrous rather than dioestrous. In both vaccinated and unvaccinated heifers, Acinetobacter spp. increased after challenge with higher abundance of Corynebacterium spp. in the vaccinated group. A total of 130 unique proteins were identified in SWATH analysis of the serum samples, and the number of differentially abundant proteins found was higher in the vaccinated group after recovery from infection compared to pre-and post-challenge (adjusted P < 0.05 and Log2FC > 0.2). Conclusion: Coglutinin, clusterin, HP homologs, vitamin D binding protein and fetuin B were identified as potential biomarkers for C. fetus venerealis infection and need further study to validate their efficiency as immune biomarkers for BGC. [ABSTRACT FROM AUTHOR]

Parasite infections are increasingly reported to change the microbiome of the parasitized hosts, while parasites bring their own microbes to what can be a multi-dimensional interaction. For instance, a recent hypothesis suggests that the microbial communities harboured by parasites may play a role in the well-documented ability of many parasites to manipulate host phenotype, and explain why the degree to which host phenotype is altered varies among conspecific parasites. Here, we explored whether the microbiomes of both hosts and parasites are associated with variation in host manipulation by parasites. Using colour quantification methods applied to digital images, we investigated colour variation among uninfected Transorchestia serrulata amphipods, as well as amphipods infected with Plagiorhynchus allisonae acanthocephalans and with a dilepidid cestode. We then characterized the bacteriota of amphipod hosts and of their parasites, looking for correlations between host phenotype and the bacterial taxa associated with hosts and parasites. We found large variation in amphipod colours, and weak support for a direct impact of parasites on the colour of their hosts. Conversely, and most interestingly, the parasite's bacteriota was more strongly correlated with colour variation among their amphipod hosts, with potential impact of amphipod-associated bacteria as well. Some bacterial taxa found associated with amphipods and parasites may have the ability to synthesize pigments, and we propose they may interact with colour determination in the amphipods. This study provides correlational support for an association between the parasite's microbiome and the evolution of host manipulation by parasites and host–parasite interactions more generally. [ABSTRACT FROM AUTHOR]

Oral neomycin administration impacts the gut microbiome and delays vitiligo development in mice, and topical antibiotics may likewise allow the microbiome to preserve skin health and delay depigmentation. Here, we examined the effects of 6‐week topical antibiotic treatment on vitiligo‐prone pmel‐1 mice. Bacitracin, Neosporin, or Vaseline were applied to one denuded flank, while the contralateral flank was treated with Vaseline in all mice. Ventral depigmentation was quantified weekly. We found that topical Neosporin treatment significantly reduced depigmentation and exhibited effects beyond the treated area, while Bacitracin ointment had no effect. Stool samples collected from four representative mice/group during treatment revealed that Neosporin treatment aligned with reduced abundance of the Alistipes genus in the gut, while relevant changes to the skin microbiome at end point were less apparent. Either antibiotic treatment led to reduced expression of MR1, potentially limiting mucosal‐associated invariant T‐cell activation, while Neosporin‐treated skin selectively revealed significantly reduced CD8+ T‐cell abundance. The latter finding aligned with reduced expression of multiple inflammatory markers and markedly increased regulatory T‐cell density. Our studies on favorable skin and oral antibiotic treatment share the neomycin compound, and in either case, microbial changes were most apparent in stool samples. Taken together, neomycin‐containing antibiotic applications can mediate skin Treg infiltration to limit vitiligo development. Our study highlights the therapeutic potential of short‐term antibiotic applications to limit depigmentation vitiligo. [ABSTRACT FROM AUTHOR]

The uterine environment provides necessary conditions for the existence of endometrial microbiota, which in turn plays an important role in maintaining the homeostasis of the uterine environment. The endometrial microbiome is highly susceptible to external factors such as age, hormones, menstrual, pregnancy, etc. When the microbiota is imbalanced, it will further promote the occurrence of uterine diseases such as endometritis and endometrial cancer. Regulating the microbiome of the endometrium is of positive significance for promoting uterine health. Among them, antibiotics, probiotics, prebiotics, and microbial transplantation may be important pathways for regulating endometrial microbiota in the future. However, there is currently no unified plan for evaluating the endometrial microbiota. In addition, due to the small sample size, it is easy to be contaminated by exogenous bacterial DNA, which poses great challenges for studying the mechanism of microbial community regulating uterine health. Therefore, there are still many areas worth exploring for the future of endometrial microbiome. [ABSTRACT FROM AUTHOR]

The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments. [ABSTRACT FROM AUTHOR]

Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation. Multiple reports point to the ability of strictly anaerobic and facultative fungi to adapt and live in anoxic subsurface. Deep-sea sediments and natural anoxic methane-emitting salty waters of sulfidic springs offer suitable habitats for developing prokaryotic-fungal microbiomes. Researchers found a billion-year-old fossil of the fungus-prokaryotic sulfate-reducing consortium buried in deep-sea biospheres. Fungal spores' ability to migrate, even after germination, through sandy layers demonstrates their potential to move up and down porous geological layers or rock fissures. Selective fungal affinity to specific wood in wood chip arrays might help differentiate viable anaerobic fungi from an anoxic environment for their rapid collection and investigation. New collection methods, cultivation, gene expression, and drug and enzyme activity analyses can boost anaerobic fungal research. [ABSTRACT FROM AUTHOR]

We report the relationship between enrichment of adapted populations and enhancement of community functional resilience in methanogenic bioreactors. Although previous studies have shown the positive effects of acclimation, this work directly investigated the relationships between microbiome dynamics and performance of anaerobic co-digesting reactors in response to different levels of an environmental perturbation (loading of grease interceptor waste [GIW]). Using the methanogenic microbiome from a full-scale digester, we developed eight sets of microbial communities in triplicate using different feed sources. These substrate-specific microbiomes were then exposed to three independent disturbance events of low-, mid- and high-GIW loading rates. This approach allowed us to directly attribute differences in community responses to differences in community composition. Despite identical inocula, environment (digester operation, substrate loading rate, and feeding patterns) and general whole-community function (methane production and effluent quality) during the cultivation period, different substrates led to different microbial community assemblies. Lipid pre-acclimation led to enrichment of a pool of specialized populations, along with thriving of sub-dominant communities. The enrichment of these populations improved functional resilience and process performance when exposed to a low level of lipid-rich perturbation compared with less-acclimated communities. At higher levels of perturbation, the communities were not able to recover methanogenesis, indicating a loading limit to the resilience response. This study extends our current understanding of environmental perturbations, feed-specific adaptation, and functional resilience in methanogenic bioreactors. [ABSTRACT FROM AUTHOR]

The microbial ecology of raw milk cheeses is determined by bacteria originating from milk and milk-producing animals. Recently, it has been shown that members of the Bifidobacterium mongoliense species may become transmitted along the Parmigiano Reggiano cheese production chain and ultimately may colonize the consumer intestine. However, there is a lack of knowledge regarding the molecular mechanisms that mediate the interaction between B. mongoliense and the human gut. Based on 128 raw milk cheeses collected from different Italian regions, we isolated and characterized 10 B. mongoliense strains. Comparative genomics allowed us to unveil the presence of enzymes required for the degradation of sialylated host-glycans in B. mongoliense, corroborating the appreciable growth on de Man-Rogosa-Sharpe (MRS) medium supplemented with 3'-sialyllactose (3'-SL) or 6'-sialyllactose (6'-SL). The B. mongoliense BMONG18 was chosen, due to its superior ability to utilize 3'-SL and mucin as representative strain, to investigate its behavior when co-inoculated with other bifidobacterial species. Conversely, members of other bifidobacterial species did not appear to benefit from the presence of BMONG18, highlighting a competitive scenario for nutrient acquisition. Transcriptomic data of BMONG18 reveal no significant differences in gene expression when cultivated in a gut simulating medium (GSM), regardless of whether cheese was included or not. Furthermore, BMONG18 was shown to exhibit high adhesion capabilities to HT29-MTX human cells, in line with its colonization ability of a human host. [ABSTRACT FROM AUTHOR]

The indicators of innate immunity and the composition of the microbiome in the nasopharyngeal mucosa in centenarians with different aging phenotypes were analyzed. A significant increase in the expression of pattern-recognizing receptor genes (TLR2, TLR4, and NLRP3) and proinflammatory cytokines (IL1B, IL18) was shown in the group of centenarians with pathological aging phenotype. In centenarians with successful aging phenotype, increased diversity of the microbiome composition was observed. At the same time, a moderate inverse correlation was found between an increase in the growth of the commensal bacterium Streptococcus salivarius and a decrease in the expression of proinflammatory cytokine genes IL1B and IL18. These findings can serve as biomarkers for the timely identification of the phenotype of aging in senile and elderly people. [ABSTRACT FROM AUTHOR]

Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing‐based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture‐independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome–immune interactions and their contributions to health and disease states. [ABSTRACT FROM AUTHOR]

A severe consequence of SARS-CoV-2 infection that manifests as systemic inflammation and multi-organ involvement is called Multisystem Inflammatory Syndrome in Children (MIS-C). This review examines the possible relationship between gut barrier integrity, the microbiome, dysregulation of interleukin 6 (IL-6) signaling, and MIS-C. Clinical and biochemical features of MIS-C are comparable to those of other hyper-inflammatory syndromes, suggesting a dysregulated immune response. One possible explanation for the systemic inflammation seen in MIS-C patients is the SARS-CoV-2-induced dysregulation of the IL-6 signaling pathway. In addition, new data suggest a reciprocal link between gut barrier integrity and IL-6. SARS-CoV-2 exhibits bacteriophage-like behavior, highlighting the role of bacteria as a reservoir for the virus and emphasizing the importance of understanding the bacteriophagic mechanism of the virus in fecal–oral transmission. The increased translocation of viral products and bacterial toxins may result from disrupting the intestinal barrier and cause systemic inflammation. On the other hand, systemic inflammation can weaken the integrity of the intestinal barrier, which feeds back into the loop of immunological dysregulation. In the context of MIS-C, understanding the interaction between SARS-CoV-2 infection, IL-6, and gut barrier integrity may shed light on the etiology of the disease and guide treatment options. Since children with gut dysbiosis may be more susceptible to MIS-C, it is critical to reinforce their microbiome through probiotics supplementation, and plant-fiber-rich diets (prebiotics). Early antibiotic treatment and the use of zonulin antagonists should also be considered. [ABSTRACT FROM AUTHOR]

Oral health remains one of the most taken for granted parts of human body health, even though poor oral health has now been linked to various diseases, such as cancers, diabetes, autoimmune complications, neurological disorders, and cardiovascular disease, just to name a few. As we review in this paper, substance use or abuse, including alcohol, smoking, recreational drugs, and pharmaceutical drugs can have significant implications on oral health, which in turn can lead to more systemic diseases. In this paper, we show that oral microbiome dysbiosis and inflammatory cytokine pathways are two of the most significant mechanisms contributing to oral health complications from substance use. When substance use decreases beneficial oral species and increases periodontopathogenic strains, a subsequent cascade of oncogenic and inflammatory cytokines is triggered. In this review, we explore these mechanisms and others to determine the consequences of substance use on oral health. The findings are of significance clinically and in research fields as the substance-use-induced deterioration of oral health significantly reduces quality of life and daily functions. Overall, the studies in this review may provide valuable information for future personalized medicine and safer alternatives to legal and pharmaceutical substances. Furthermore, they can lead towards better rehabilitation or preventative initiatives and policies, as it is critical for healthcare and addiction aid specialists to have proper tools at their disposal. [ABSTRACT FROM AUTHOR]

It is imperative to say that we are immersed in a sea of microorganisms due to their ubiquitous presence on the planet, from soil to water and air. Human bodies harbor a vast array of microorganisms from both the inside and out called the human microbiome. It is composed of single-celled organisms, including archaea, fungi, viruses, and bacteria, including bacteriophages, where bacteria are the biggest players, and this is collectively referred to as the human microbiome. These organisms have a symbiotic relationship with humans and impact human physiology where they colonize various sites on and in the human body, adapting to specific features of each niche. However, dysbiosis, or the deviation from normal microbial composition, is associated with adverse health effects, disrupted ecosystems, and eco-imbalance in nature. In this review, we delve into the comprehensive oversight of bacteria, their cosmopolitan presence, and their additional applications affecting human lives. [ABSTRACT FROM AUTHOR]

The gut, urine, and vaginal microbiomes play significant roles in the pathogenesis of recurrent urinary tract infections (rUTIs). Analysis of these microbiota has shown distinct associations with urinary tract infections. Encouraging data indicate that rUTIs may be responsive to microbiome treatments such as fecal microbiota transplantation, expanding potential treatments beyond antibiotics, hydration, and behavioral interventions. If successful, these nonantibiotic therapies have the potential to increase time between rUTI episodes and reduce the prevalence of multidrug-resistant organisms. In this review, we discuss the role of the 3 microbiomes in the pathogenesis of rUTI and utilization of live biotherapeutic products as therapy for rUTI. [ABSTRACT FROM AUTHOR]

Objective: Anorexia nervosa has the highest mortality rate among psychiatric illnesses. Current treatments remain ineffective for a large fraction of patients. This may be due to unclear mechanisms behind its development and maintenance. Studies exploring the role of the gut microbiome have revealed inconsistent evidence of dysbiosis. This article aims to investigate changes in the gut microbiome, particularly, mean differences in the Firmicutes to Bacteroidetes ratio, in adolescent and adult individuals with anorexia nervosa following inpatient treatment. Methods: Longitudinal studies investigating gut microbiome composition in inpatient populations of anorexia nervosa before and after treatment were systematically reviewed. Additionally, gut microbiome compositions were characterized in three acute anorexia nervosa inpatients early after admission and after 4–12 weeks of treatment. Results: Review results indicated an increase in the Firmicutes to Bacteroidetes ratio in individuals with anorexia nervosa after treatment. These however did not match values of their healthy counterparts. In the case‐series samples, the reverse occurred with samples taken 4 weeks after treatment. In the patient who provided an extra sample 12 weeks after treatment, similar results to the studies included in the review were observed. Furthermore, Firmicutes to Bacteroidetes ratio values in the case‐series samples were notably higher in the two patients who had chronic anorexia nervosa. Discussion: Differences in methodologies, small sample sizes, and insufficient data limited the generalizability of the outcomes of the reviewed studies. Results suggest a potentially unique microbiome signature in individuals with chronic anorexia nervosa, which may explain different outcomes in this group of patients. [ABSTRACT FROM AUTHOR]

The emergence of mRNA vaccines for SARS-CoV-2 has opened a new page in vaccine development. Nevertheless, concerns of experts have been expressed about unintentional side effects on the gut microbiota (GM). Previous studies showed that this virus acts as a bacteriophage, which infects and destroys specific bacterial strains in the GM. The present manuscript hypothesizes that the synthetic spike protein could create changes in the composition and the functioning of the GM by entering the intestinal cells after vaccination and impairing the symbiotic relationship between intestinal cells and the GM. An experimental protocol to test the hypothesis is suggested. [ABSTRACT FROM AUTHOR]