Specific Microbial Taxa Research Articles

Sex-Induced Changes in Microbial Eukaryotes and Prokaryotes in Gastrointestinal Tract of Simmental Cattle

This study investigates gender-based differences in the gut microbiota of Simmental cattle, focusing on bacterial, archaeal, and fungal communities. Fecal samples were collected and analyzed using high-throughput sequencing, with taxonomic classification performed through the SILVA and UNITE databases. Alpha and beta diversity metrics were assessed, revealing significant differences in the diversity and composition of archaeal communities between males and females. Notably, females exhibited higher alpha diversity in archaea, while beta diversity analyses indicated distinct clustering of bacterial and archaeal communities by gender. The study also identified correlations between specific microbial taxa and hematological parameters, with Treponema and Methanosphaera showing gender-specific associations that may influence cattle health and productivity. These findings highlight the importance of considering gender in microbiota-related research and suggest that gender-specific management strategies could optimize livestock performance. Future research should explore the role of sex hormones in shaping these microbial differences.

The intra-tumoral microbiome as a potential biomarker of response to external beam radiation therapy in cervical cancer

BackgroundWe aimed to determine the potential predictive value of the intra-tumoral microbiome as a marker of the response to external beam radiation therapy (EBRT) in cervical cancer (CC).MethodsA prospective longitudinal trial of 36 CC patients receiving pelvic radiotherapy was designed to investigate microbial characteristic signatures and diversity (alpha and beta) of multiple sites (tumor, vaginal, gut, urethral, and oral) in the superior response (SR) and inferior response (IR) groups of CC patients by 16S rRNA sequencing. Utilized the least absolute shrinkage and selection operator (LASSO) logistic regression method to analyze clinicopathological factors that potentially influenced the efficacy of EBRT. LEfSe analysis highlighted the microbiome features that best distinguished the categorized patient samples. Selected parameters were validated with Spearman correlation analysis, receiver operating characteristic (ROC) area under the curve (AUC) analysis and Kaplan-Meier survival analysis.ResultsFirstly, in our cohort, LASSO logistic regression analysis revealed no association between clinicopathological factors and EBRT efficacy. Subsequently, we employed 16S rRNA sequencing to compare microbiome differences across multiple sites and their correlations with major clinicopathological factors. We discovered that the intra-tumoral microbiome was independent of clinicopathologic features and represented the most direct and reliable reflection of the microbial differences between the SR and IR groups. We found lower alpha diversity in the tumor microbiome of SR group and identified the most relevant microbiome taxa (Bifidobacteriaceae, Beijerinckiaceae, and Orbaceae) associated with the efficacy of the response to EBRT in CC patients. We then conducted ROC analysis, finding that specific microbial taxa had an AUC of 0.831 (95% CI, 0.667–0.995), indicating the potential of these taxa as biomarkers for predicting EBRT efficacy. Kaplan-Meier survival analysis showed a better prognosis for patients with lower alpha diversity and higher relative abundance of Bifidobacteriaceae.ConclusionsOur data suggested that intra-tumoral specific microbiome taxa and lower alpha diversity may play an important role in the CC patient sensitivity to EBRT and offer novel potential biomarkers for predicting the response to EBRT efficacy.

Microbial biomarker discovery in Parkinson’s disease through a network-based approach

Associations between the gut microbiota and Parkinson’s disease (PD) have been widely investigated. However, the replicable biomarkers for PD diagnosis across multiple populations remain elusive. Herein, we performed a meta-analysis to investigate the pivotal role of the gut microbiome in PD and its potential diagnostic implications. Six 16S rRNA gene amplicon sequence datasets from five independent studies were integrated, encompassing 550 PD and 456 healthy control samples. The analysis revealed significant alterations in microbial composition and alpha and beta diversity, emphasizing altered gut microbiota in PD. Specific microbial taxa, including Faecalibacterium, Roseburia, and Coprococcus_2, known as butyrate producers, were notably diminished in PD, potentially contributing to intestinal inflammation. Conversely, genera such as Akkermansia and Bilophila exhibited increased relative abundances. A network-based algorithm called NetMoss was utilized to identify potential biomarkers of PD. Afterwards, a classification model incorporating 11 optimized genera demonstrated high performance. Further functional analyses indicated enrichment in pathways related to neurodegeneration and metabolic pathways. These findings illuminate the intricate relationship between the gut microbiota and PD, offering insights into potential therapeutic interventions and personalized diagnostic strategies.

Leaf age structures phyllosphere microbial communities in the field and greenhouse.

The structure of the leaf microbiome can alter host fitness and change in response to abiotic and biotic factors, like seasonality, climate, and leaf age. However, relatively few studies consider the influence of host age on microbial communities at a time scale of a few days, a short time scale relevant to microbes. To understand how host age modulates changes in the fungal and bacterial leaf microbiome on a short time scale, we ran independent field and greenhouse-based studies and characterized phyllosphere communities using next-generation sequencing approaches. Our field study characterized changes in the fungal and bacterial phyllosphere by examining leaves of different relative ages across individuals, whereas the greenhouse study examined changes in the fungal microbiome by absolute leaf age across individuals. Together, these results indicate that fungal communities are susceptible to change as a leaf ages as evidenced by shifts in the diversity of fungal taxa both in the field and the greenhouse. Similarly, there were increases in the diversity of fungal taxa by leaf age in the greenhouse. In bacterial communities in the field, we observed changes in the diversity, composition, and relative abundance of common taxa. These findings build upon previous literature characterizing host-associated communities at longer time scales and provide a foundation for targeted work examining how specific microbial taxa might interact with each other, such as fine-scale interactions between pathogenic and non-pathogenic species.

Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.

O-277 Exploring the relationship between the vaginal microbiota and vaginal symptoms

Abstract Study question What is the relationship between self-reported vaginal symptoms and the composition of the vaginal microbiome? Summary answer Our study reveals a complex and multifactorial relationship between vaginal symptoms and the composition of the vaginal microbiome. What is known already Vaginal dysbiosis (VD) is a microbial condition characterized by the absence of beneficial lactobacilli and the presence of pathogenic bacteria in the vagina. VD is associated with elevated risks of sexually transmitted infections, preterm birth, pregnancy loss, infertility, and suboptimal outcomes in in vitro fertilization. Clinical manifestations often include increased vaginal discharge and malodour, although it’s noteworthy that a substantial proportion of women with VD remain asymptomatic, which makes diagnosing these women challenging. Study design, size, duration Our study was conducted as part of a Double-Blinded Randomized Controlled Trial (RCT) evaluating Vaginal Microbiota Transplantation (VMT) as a novel approach for treating vaginal dysbiosis without antibiotics. This study included 263 women aged 18-40 years. Participants/materials, setting, methods We employed shotgun metagenomic sequencing to analyse the vaginal microbiome on cycle day 10+/-2 days. Moreover, we collected data on vaginal symptoms, hormonal contraceptive use, and sexual behaviour. Main results and the role of chance Among the 263 participants, 65% exhibited eubiotic microbiomes, 23% had dysbiotic microbiomes, and 12% had intermediate microbiomes. Vaginal symptoms were reported by 33%, while 63% remained symptom-free. In terms of dominance, L. crispatus dominated in 40% of samples, followed by L. iners (30%) and G. vaginalis (9.1%). In symptomatic women, L. iners (22%) and L. crispatus (21%) were common taxa, while asymptomatic women showed higher prevalence of these taxa: L. crispatus (50%) and L. iners (34%). Symptoms analysis showed two significant clusters dominated by L. crispatus or L. iners, along with smaller dysbiotic clusters led by G. vaginalis and F. vaginae. Dysbiotic samples exhibited higher rates of increased discharge and malodor, while stinging and itching were more prevalent in eubiotic samples. Positive associations were noted between specific microbial taxa and distinct symptoms. Exploring external factors, contraceptive use revealed weak associations with microbial changes. Sexual behavior patterns also influenced microbial composition, notably in women with varying numbers of male sexual partners within the last 3 months. These findings provide valuable insights into the intricate interactions between vaginal microbiota, symptoms, and external factors, shedding light on the complex landscape of vaginal dysbiosis. Limitations, reasons for caution Our study is limited by the cross-sectional design, and causality cannot be inferred. Self-reporting of symptoms may introduce bias. Additionally, our findings may not be generalizable to all populations sin the majority of the women in our cohort are younger and likely to have higher education Wider implications of the findings Our findings highlight the complexity of VD symptomatology and underscore the need for further research into the relationship between vaginal symptoms, microbiota and clinical outcomes. Trial registration number NCT04855006

Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions.

Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral-algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral-algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.

The microbiota characterizing huge carbonatic moonmilk structures and its correlation with preserved organic matter

BackgroundMoonmilk represents complex secondary structures and model systems to investigate the interaction between microorganisms and carbonatic rocks. Grotta Nera is characterized by numerous moonmilk speleothems of exceptional size hanging from the ceiling, reaching over two meters in length. In this work we combined microbiological analyses with analytical pyrolysis and carbon stable isotope data to determine the molecular composition of these complex moonmilk structures as well as the composition of the associated microbiota.ResultsThree moonmilk structures were dissected into the apical, lateral, and core parts, which shared similar values of microbial abundance, richness, and carbon isotopes but different water content, microbiota composition, and organic matter. Moonmilk parts/niches showed higher values of microbial biomass and biodiversity compared to the bedrock (not showing moonmilk development signs) and the waters (collected below dripping moonmilk), indicating the presence of more complex microbial communities linked to carbonate rock interactions and biomineralization processes. Although each moonmilk niche was characterized by a specific microbiota as well as a distinct organic carbon profile, statistical analyses clustered the samples in two main groups, one including the moonmilk lateral part and the bedrock and the other including the core and apical parts of the speleothem. The organic matter profile of both these groups showed two well-differentiated organic carbon groups, one from cave microbial activity and the other from the leaching of vascular plant litter above the cave. Correlation between organic matter composition and microbial taxa in the different moonmilk niches were found, linking the presence of condensed organic compounds in the apical part with the orders Nitrospirales and Nitrosopumilales, while different taxa were correlated with aromatic, lignin, and polysaccharides in the moonmilk core. These findings are in line with the metabolic potential of these microbial taxa suggesting how the molecular composition of the preserved organic matter drives the microbiota colonizing the different moonmilk niches. Furthermore, distinct bacterial and archaeal taxa known to be involved in the metabolism of inorganic nitrogen and C1 gases (CO2 and CH4) (Nitrospira, Nitrosopumilaceae, Nitrosomonadaceae, Nitrosococcaceae, and novel taxa of Methylomirabilota and Methanomassiliicoccales) were enriched in the core and apical parts of the moonmilk, probably in association with their contribution to biogeochemical cycles in Grotta Nera ecosystem and moonmilk development.ConclusionsThe moonmilk deposits can be divided into diverse niches following oxygen and water gradients, which are characterized by specific microbial taxa and organic matter composition originating from microbial activities or deriving from soil and vegetation above the cave. The metabolic capacities allowing the biodegradation of complex polymers from the vegetation above the cave and the use of inorganic nitrogen and atmospheric gases might have fueled the development of complex microbial communities that, by interacting with the carbonatic rock, led to the formation of these massive moonmilk speleothems in Grotta Nera.

Short impact on soil microbiome of a Bacillus amyloliquefaciens QST713 based product that correlates with higher potato yield across USA.

Potato (Solanum tuberosum L.) is considered one of the most widely consumed crops worldwide, due to its high yield and nutritional profile, climate change-related environmental threats and increasing food demand. This scenario highlights the need of sustainable agricultural practices to enhance potato productivity, while preserving and maintaining soil health. Plant growth-promoting bacteria (PGPB) stimulate crop production through biofertilization mechanisms with low environmental impact. For instance, PGPB promote biological nitrogen fixation, phosphate solubilization, production of phytohormones, and biocontrol processes. Hence, these microbes provide a promising solution for more productive and sustainable agriculture. In this study, the effects of Bacillus amyloliquefaciens QST713 based-product (MINUET™, Bayer) were assessed in terms of yield, soil microbiome, potato peel and petiole nutrient profile as a promising PGPB in a wide range of potato cultivars across the United States of America. Depending on the location, potato yield and boron petiole content increased after biostimulant inoculation to maximum of 24% and 14%, respectively. Similarly, nutrient profile in potato peel was greatly improved depending on the location with a maximum of 73%, 62% and 36% for manganese, zinc and phosphorus. Notably, fungal composition was shifted in the treated group. Yield showed strong associations with specific microbial taxa, such as Pseudoarthrobacter, Ammoniphilus, Ideonella, Candidatus Berkiella, Dongia. Moreover, local networks strongly associated with yield, highlighting the important role of the native soil microbiome structure in indirectly maintaining soil health. Our results showed that treatment with B. amyloliquefaciens based product correlated with enhanced yield, with minor impacts on the soil microbiome diversity. Further studies are suggested to disentangle the underlying mechanisms of identified patterns and associations.

Vertical transmission of microbiomes into embryo culture media and its association with assisted reproductive outcomes

Research Question: Can microbes vertically transmit from semen and follicular fluids to embryo culture media during assisted reproductive technology (ART) treatments?Design: Spent embryo culture media (SECM) were collected along with seminal fluid and follicular fluid samples from 61 infertility couples undergoing ART treatment at the Prince of Wales Hospital, Hong Kong SAR, China. Metagenomic analysis was conducted to identify the source of microbes in SECM, the correlation between semen microbiomes and male infertility, and the correlation between follicular fluid microbiome and female infertility.Results: Microbial vertical transmission into SECM was reported in 82.5% of the cases, and semen was the main source of contamination in c-IVF cases. The increased abundances of Staphylococcus and Streptococcus anginosus in semen showed statistically negative impacts on sperm count and total motility, respectively (p <0.001). We observed significant increases in the abundances of Prophyromonas, Neisseria, and Facklamia in follicular fluid in women with anovulation, uterine factor infertility, and unexplained infertility, respectively (p <0.01). Finally, there was no significant correlation between the bacteria identified in all sample types with ART outcomes including fertilization rates, embryo development, the number of available embryos, and clinical pregnancy rates.Conclusion: Embryo culture media can be contaminated during ART treatment, not only by seminal microbes but also by follicular fluid and other sources of microbes. There were strong correlations between specific microbial taxa in semen and sperm quality as well as between follicular fluid microbiomes and the etiology of female infertility. However, the microbiome of SECM, semen, and follicular fluid showed no significant association with ART treatment outcomes.

The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses.

In the evolving landscape of cancer research, the human microbiome emerges as a pivotal determinant reshaping our understanding of tumorigenesis and therapeutic responses. Advanced sequencing technologies have uncovered a vibrant microbial community not confined to the gut but thriving within tumor tissues. Comprising bacteria, viruses, and fungi, this diverse microbiota displays distinct signatures across various cancers, with most research primarily focusing on bacteria. The correlations between specific microbial taxa within different cancer types underscore their pivotal roles in driving tumorigenesis and influencing therapeutic responses, particularly in chemotherapy and immunotherapy. This review amalgamates recent discoveries, emphasizing the translocation of the oral microbiome to the gut as a potential marker for microbiome dysbiosis across diverse cancer types and delves into potential mechanisms contributing to cancer promotion. Furthermore, it highlights the adverse effects of the microbiome on cancer development while exploring its potential in fortifying strategies for cancer prevention and treatment.

Exploring reciprocal causation: bidirectional mendelian randomization study of gut microbiota composition and thyroid cancer

BackgroundWhile an association between gut microbiota composition and thyroid cancer (TC) has been observed, the directionality and causality of this relationship remain unclear.MethodsWe conducted a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal effect between gut microbiota composition and TC. Gut microbiota data were derived from a diverse population encompassing various ethnicities (n = 18,340 samples), while TC data were sourced from an European population (n = 218,792 samples). Instrumental variables, represented by single nucleotide polymorphisms (SNPs), were employed to assess the causal relationship using multiple MR methods, including inverse-variance weighting (IVW), weighted median, weighted mode, MR-Egger, and simple mode. F-statistics and sensitivity analyses were performed to evaluate the robustness of the findings.ResultsOur investigation identified a comprehensive set of 2934 instrumental variables significantly linked to gut microbiota composition (p < 1 × 10-5). The analysis illuminated notable candidates within the phylum Euryarchaeota, including families Christensenellaceae and Victivallaceae, and genera Methanobrevibacter, Ruminococcus2, and Subdoligranulum, which emerged as potential risk factors for TC. On the other hand, a protective influence against TC was attributed to class Betaproteobacteria, family FamilyXI, and genera Anaerofilum, Odoribacter, and Sutterella, alongside order Burkholderiales. Further enhancing our insights, the integration of 7 instrumental variables from TC data (p < 1 × 10-5) disclosed the regulatory potential of one family and five genera. Notably, the genus Coprobacter innocuum group (p = 0.012, OR = 0.944) exhibited the highest probability of regulation. Our meticulous analyses remained free from significant bias, heterogeneity, or horizontal pleiotropy concerns.ConclusionThrough a bidirectional two-sample Mendelian randomization approach, we elucidated a potential bidirectional causal relationship between gut microbiota composition and TC. Specific microbial taxa were associated with an increased risk or conferred protection against TC. These findings advance our understanding of the complex interplay between the gut microbiota and TC pathogenesis, offering new insights into the therapeutic potential of modulating the gut microbiota for managing TC.

P1242 Pediatric IBD microbiome and microbial profiles formed within the family

Abstract Background The rise of microbiome-focused research, reveals that the intrafamilial microbiome can be linked to specific genetic traits and be studied for its behavior during dysbiosis. It has been reported that microbiota composition is shared between cohabitating individualsand displays patterns of similarity that differ between families. Based on these observations, this study focuses on treatment-naïve pediatric IBD patients and their immediate families to identify the role of the microbiome in disease onset. Methods Families with pediatric IBD were recruited,comprising seven drug-naïve Crohn’s disease (CD) patients and two drug-naïve ulcerative colitis (UC) patients, as well as healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing and bioinformatics analysis. Results Our results elucidate the fact that even though family members share lifestyle and dietary habits, the patients exhibit unique microbiome patterns which could only be attributed to the disease. In addition, we studiedthe impact of the disease on specific microbial taxa and how these could serve as potential biomarkers for early detection. Conclusion We found a potential role of maternal factors in the establishment and modulation of the early life microbiome, consistent with the current literature, which may have implications for understanding the etiology and progression of IBD.

Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis.

The emergent recognition of the gut-brain axis connection has shed light on the role of the microbiota in modulating the gut-brain axis's functions. Several microbial metabolites, such as serotonin, kynurenine, tryptamine, indole, and their derivatives originating from tryptophan metabolism have been implicated in influencing this axis. In our study, we aimed to investigate the impact of running exercises on microbial tryptophan metabolism using a mouse model. We conducted a multi-omics analysis to obtain a comprehensive insight into the changes in tryptophan metabolism along the microbiota-gut-brain axis induced by running exercises. The analyses integrated multiple components, such as tryptophan changes and metabolite levels in the gut, blood, hippocampus, and brainstem. Fecal microbiota analysis aimed to examine the composition and diversity of the gut microbiota, and taxon-function analysis explored the associations between specific microbial taxa and functional activities in tryptophan metabolism. Our findings revealed significant alterations in tryptophan metabolism across multiple sites, including the gut, blood, hippocampus, and brainstem. The outcomes indicate a shift in microbiota diversity and tryptophan metabolizing capabilities within the running group, linked to increased tryptophan transportation to the hippocampus and brainstem through circulation. Moreover, the symbiotic association between Romboutsia and A. muciniphila indicated their potential contribution to modifying the gut microenvironment and influencing tryptophan transport to the hippocampus and brainstem. These findings have potential applications for developing microbiota-based approaches in the context of exercise for neurological diseases, especially on mental health and overall well-being.

Causal Relationship between Gut Microbiota and Aneurysm: A Mendelian Randomization Study

Introduction: Observational studies have suggested a possible relationship between gut microbiota (GM) and aneurysm development. However, the nature of this association remains unclear due to the inherent limitations of observational research, such as reverse causation and confounding factors. To address this knowledge deficit, this study aimed to investigate and establish a causal link between GM and aneurysm development. Methods: Summary statistics regarding GM and aneurysms were collected from relevant genome-wide association studies. Two samples were used in mendelian randomization (MR). The principal MR technique utilized was inverse-variance weighting, a technique renowned for producing reliable causal effect estimations. Additional MR methods, including weighted median (WM), MR-Egger, MR-PRESSO, and simple mode methods, were employed to ensure the robustness of the aforementioned association and investigate potential biases. Sensitivity analyses were performed to determine the consistency of the MR findings. Results: Varying associations were observed between specific microbial taxa and the different aneurysms analyzed. A negative correlation was observed between aortic aneurysm (AA) and Lentisphaerae, Lentisphaeria, and Victivallales. Conversely, the genus FamilyXIIIUCG001 exhibited an increased risk association. Regarding abdominal AA, Victivallaceae showed a reduced risk, and Bilophila and Catenibacterium were associated with an increased risk. For thoracic AA, negative and positive correlations were observed with Lentisphaerae and Turicibacter, respectively. Lastly, in the case of cerebral aneurysm (CA), Firmicutes and Haemophilus were associated with a decreased risk, and Lachnoclostridium demonstrated an increased risk of association. Conclusion: Our research has established causal relationships between specific GM components and various aneurysms. The obtained knowledge may aid in the development of microbiome-based interventions and the identification of novel biomarkers for targeted prevention strategies.

Soil priming effects and involved microbial community along salt gradients

Abstract. Soil salinity mediates microorganisms and soil processes, like soil organic carbon (SOC) cycling. Yet, how soil salinity affects SOC mineralization via shaping bacterial community diversity and composition remains elusive. Therefore, soils were sampled along a salt gradient (salinity at 0.25 %, 0.58 %, 0.75 %, 1.00 %, and 2.64 %) and incubated for 90 d to investigate (i) SOC mineralization (i.e., soil priming effects induced by cottonseed meal, as substrate) and (ii) the responsible bacteria community by using high-throughput sequencing and natural abundance of 13C isotopes (to partition cottonseed-meal-derived CO2 and soil-derived CO2). We observed a negative priming effect during the first 28 d of incubation that turned to a positive priming effect after day 56. Negative priming at the early stage might be due to the preferential utilization of cottonseed meal. The followed positive priming decreased with the increase in salinity, which might be caused by the decreased α diversity of microbial communities in soil with high salinity. Specifically, soil pH and electrical conductivity (EC) along the salinity gradient were the dominant variables modulating the structure of the microbial community and consequently SOC priming (estimated by distance-based multivariate analysis and path analysis). By adopting two-way orthogonal projections to latent structures (O2PLS), priming effects were linked with specific microbial taxa; e.g., Proteobacteria (Luteimonas, Hoeflea, and Stenotrophomonas) were the core microbial genera that were attributed to the substrate-induced priming effects. Here, we highlight that the increase in salinity reduced the diversity of the microbial community and shifted dominant microorganisms (Actinobacteria and Proteobacteria: Luteimonas, Hoeflea, and Stenotrophomonas) that determined SOC priming effects, which provides a theoretical basis for understanding SOC dynamics and microbial drivers under the salinity gradient.

Inflammatory Manifestations Associated With Gut Dysbiosis in Alzheimer's Disease.

Recent studies strongly suggest that gut microbiome can influence brain functions and contribute to the development of Alzheimer's disease (AD). However, reported changes in the gut microbiomes in AD patients from different countries are not similar, and more research is needed to reveal the relationships between human microbiomes and AD in diverse ethnic populations. There is also an assumption that microbiome-associated peripheral inflammation might drive the development of sporadic AD. This cross-sectional study is aimed at analyzing the gut microbial profile and exploring potential associations with blood cytokines and some clinical parameters among individuals diagnosed with Alzheimer's in Kazakhstan. Consistent with previous studies, we have found that the microbial landscape in AD reveals specific alterations in the gut microbiome. Specifically, the AD patient group showed a decreased Firmicutes/Bacteroidetes ratio. The differential abundance analysis highlighted a dysbiosis in the gut microbiota of AD patients, marked by a reduced presence of Bifidobacterium, particularly B. breve. In our study, AD patients' altered gut microbiota composition notably features an increased presence of Pseudomonadota like Phyllobacterium and inflammatory bacteria such as Synergistetes and the Christensenellaceae family. The metabolic profiling of the AD microbiome reveals a predominant presence of pathways related to sugar, carrier molecules, tetrapyrrole, pyrimidine biosynthesis, and nucleic acid processing. This analysis also highlighted a marked reduction in SCFA, carbohydrate, polysaccharide, polyamine, and myo-inositol degradation pathways. The increases in the proinflammatory cytokines IL-1a, IL-8, IL-17A, IL-12p40, TNF-β, MCP-1, IL-2, and IL-12p70 and the anti-inflammatory cytokines IL-10 and IL-13 were observed in AD patients. Key variables driving the separation of AD and controls include inflammatory markers (IL-1a and IL-8), growth factors (EGF), lipids (LDL), BMI, and gut microbes, like genus Tyzzerella and Turicibacter and species Parabacteroides distasonis and Bacteroides eggerthii. We have also demonstrated that almost all cytokines strongly correlate with serum adiponectin levels and specific microbial taxa in AD patients. Thus, our findings identify potential microbial and inflammatory signatures in an ethnically distinct cohort of AD patients. These could serve as AD biomarkers and microbiota-based therapeutic targets for treating AD.

Causal Associations Between the Gut Microbiome and Aortic Aneurysm: A Mendelian Randomization Study

Background: Observational studies have indicated an association between the gut microbiota and the occurrence and progression of aortic aneurysm (AA). However, the causal relationship between the gut microbiota and AA and its subtypes remains unclear. This study used Mendelian randomization (MR) to gain new insights into the relationship between the gut microbiota and AA, including AA subtypes. Methods: We used summary data from a genome-wide association study of gut microbiota to determine genetically predicted microbial taxa. Additionally, we predicted causal relationships between the gut microbiota and AA, including AA subtypes. MR was conducted with two-sample MR with the inverse variance weighting, MR-Egger, weighted median, and weighted mode methods to assess the causal relationships. Heterogeneity and pleiotropy were evaluated with the MR-Egger method, Cochran’s Q test, and the MR-PRESSO Global test. The strength of the causal relationships between exposures and outcomes was assessed with Bonferroni correction. The stability of the MR results was evaluated with leave-one-out analyses. Reverse MR analysis was also performed to examine reverse causality. Results: Through MR analysis, after Bonferroni correction, specific microbial taxa were found to have a causal relationship in AA and its subtypes. Specifically, the phylum Lentisphaerae (OR = 0.82, P = 0.001), class Lentisphaeria (OR = 0.81, P = 0.0028), and family Bifidobacteriaceae (OR = 0.79, P &lt; 0.001) were negatively associated with AA risk, whereas the genus Family XIII UCG001 (OR = 1.33, P &lt; 0.001) was positively associated with AA risk. Regarding subtypes, elevated levels of the genus Bilophila (OR = 1.36, P &lt; 0.001) were closely associated with abdominal aortic aneurysm (AAA) occurrence. Lower levels of the family Bifidobacteriaceae (OR = 0.71, P &lt; 0.001) and phylum Lentisphaerae (OR = 0.81, P = 0.0025), and higher levels of the genus Ruminococcaceae UCG014 (OR = 1.30, P &lt; 0.001) exhibited strong causal relationships with thoracic aortic aneurysm (TAA). Conclusion: Our study suggests that specific components of the gut microbiota have causal effects, either beneficial or detrimental, on AA risk, thus providing potentially valuable biomarkers for early diagnosis and potential therapeutic targets.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle.

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

Correlation between microbial communities and volatile organic compounds in an urban soil provides clues on soil quality towards sustainability of city flowerbeds

Soil functionality is critical to the biosphere as it provides ecosystem services relevant for a healthy planet. The soil microbial composition is significantly impacted by anthropogenic activities, including urbanization. In this context, the study of soil microorganisms associated to urban green spaces has started to be crucial toward sustainable city development. Microbes living in the soil produce and degrade volatile organic compounds (VOCs). The VOC profiles may be used to distinguish between soils with various characteristics and management practices, reflecting variations in the activity of soil microbes that use a variety of metabolic pathways. Here, a combined approach based on DNA metabarcoding and GC-MS analysis was used to evaluate the soil quality from urban flowerbeds in Prato (Tuscany, Italy) in terms of microbial biodiversity and VOC emission profiles, with the final aim of evaluating the possible correlation between composition of microbial community and VOC patterns. Results showed that VOCs in the considered soil originated from anthropic and biological activity, and significant correlations between specific microbial taxa and VOCs were detected. Overall, the study demonstrated the feasibility of the use of microbe-VOC correlation as a proxy for soil quality assessment in urban soils.