Changes In Relative Abundance Research Articles

Individual variation of boldness in free-ranging bottlenose dolphins (Tursiops truncatus) interacting with scuba divers in French Polynesia

Marine wildlife tourism is known to affect target species across multiple spatial and temporal scales, from short-term behavioral responses to changes in relative abundance and habitat use patterns. However, despite a growing number of population-, community-, and group-level studies, a limited number of them have focused their research on individual responses to wildlife tourism, particularly on free-ranging cetaceans.Between 2018 and 2020, we investigated the behavioral responses of 20 non-provisioned bottlenose dolphins (Tursiops truncatus) to recreational scuba divers in Rangiroa Atoll, French Polynesia, to understand whether these individuals that had been repeatedly exposed to scuba diving tourism on at least one year exhibited temperament traits along the ‘shyness-boldness’ axis. We also considered potential variation in boldness in relation to sex, age, and tourist-site fidelity.The study documented individual differences in the dolphins’ boldness. There was no variation in boldness according to sex and tourist-site fidelity, but age significantly influenced the dolphins’ boldness with immature dolphins being bolder than mature individuals. The more extreme case of boldness involved four dolphins that tolerated repeated physical interactions with scuba divers.In Rangiroa, scuba diving tourism promotes repeated intrusive interactions with dolphins that might make bold individuals particularly vulnerable to collateral threats associated with human activities. It is therefore crucial to consider individual variation in the dolphins’ behavioral responses to tourism to implement optimal tourism management measures. We suggest in the discussion recommendations to help minimize the risks for both the dolphins and humans associated with repeated close interactions.

Genes involved in carbon, nitrogen, and sulfur cycling in an important estuarine ecosystem show coherent shifts in response to changes in environmental conditions

AbstractWhile metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process.

Metabolic and Physiological Effects of Antibiotic-Induced Dysbiosis in Citrus

Streptomycin (Str) and oxytetracycline (Otc) are widely used antibiotics to manage bacterial diseases in citrus and other crops. However, their impacts on the rhizosphere bacterial assembly and plant physiology are poorly understood. The aim of this study was to examine the effects of Str and Otc on the physiology (assimilation, transpiration rate, intracellular CO2, and stomatal conductance to water vapor), rhizosphere bacterial assemblages (16S rRNA gene high-throughput amplicon sequencing), and rhizosphere metabolite profiles in healthy Citrus reticulata trees. The results indicated a reduction in photosynthesis after Str and Otc treatments, whereas CO2 outflow stayed constant. Both antibiotics decreased the culturable numbers of bacteria. Analysis of the microbiome showed changes in relative abundance of bacterial groups, specifically Pseudomonas, Agrobacterium, and Streptomyces, in response to the antibiotics. Metabolite profiles changed in streptomycin- and oxytetracycline-treated citrus plants suggesting response to microbe targets or induction of stress responses. This study advances knowledge of antibiotic-driven effects on the rhizosphere microbiome, rhizosphere metabolome, and plant physiology, which is essential for managing plant diseases while safeguarding rhizosphere ecology and long-term plant health.

Heavy metal exposure reduces larval gut microbiota diversity of the rice striped stem borer, Chilo suppressalis.

Cadmium (Cd), a widely distributed environmental pollutant in agroecosystems, causes negative effects on crops and herbivores through bottom-up processes. The gut microbial community of an insect can play a critical role in response to metal stress. To understand how microbiota affect the stress responses of organisms to heavy metals in agroecosystems, we initially used 16S rRNA sequencing to characterize the larval gut microbiota of Chilo suppressalis, an important agricultural pest, exposed to a diet containing Cd. The species richness, diversity, and composition of the gut microbial community was then analyzed. Results revealed that while the richness (Chao1 and ACE) of gut microbiota in larvae exposed to Cd was not significantly affected, diversity (Shannon and Simpson) was reduced due to changes in species distribution and relative abundance. Overall, the most abundant genus was Enterococcus, while the abundance of the genera Micrococcaceae and Faecalibaculum in the control significantly superior to that in Cd-exposed pests. Phylogenetic investigation of microbial communities by the reconstruction of unobserved states (PICRUSt) showed that the intestinal microorganisms appear to participate in 34 pathways, especially those used in environmental information processing and the metabolism of the organism. This study suggests that the gut microbiota of C. suppressalis are significantly impacted by Cd exposure and highlights the importance of the gut microbiome in host stress responses and negative effects of Cd pollution in agroecosystems.

Understanding the ecological versatility of Tetracladium species in temperate forest soils.

Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.

Alteration of the gut microbiota changes during the one-year Antarctic deployment in a group of Chinese Han population

BackgroundIt is common knowledge that people’s intestinal microbiota is significantly influenced by the external environment. Although the Antarctic continent has been discovered for nearly 200 years, it is still unclear how this environment affects the human intestinal microbiota, especially that of the Chinese Han population.MethodsTwelve explorers underwent a one-year Antarctic deployment from December 2017 to December 2018. The gut microbiota and clinical indexes at five time points, including two months (T1), five months (T2), eight months (T3), 11 months (T4) of residence in Antarctica and 7 months after returning to China (T5), were investigated.ResultsThe intestinal microbiota of the participants was changed after one-year Antarctic deployment even after they left Antarctica. For the microbiota tested after returning to China (T5), the amount of Citrobacter, Akkermansia and conditional pathogens such as Escherichia-Shigella increased significantly (P < 0.05). The concentration of the major biochemical indicators in the serum exhibited an increasing trend before T3, and decreased significantly at T4. When tested again at T5, most of the serum concentrations increased, only 5-hydroxytryptamine was significantly decreased. Spearman correlation analysis showed the change in the relative abundance of Anaerotruncus was negatively associated with the changes in the concentration of total thyroxine, alanine transaminase, γ-glutamyl transpeptidase, serum cystatin C and apolipoprotein A1. The relative abundance change in Citrobacter was positively associated with the change in the concentration of uric acid.ConclusionBy objectively analyzing the influence of the Antarctic environment on the change of intestinal microbiota, we were able to provide theoretical support for subsequent Antarctic related research.

Complementarity and sensitivity of benthic state indicators to bottom-trawl fishing disturbance.

Many indicators have been developed to assess the state of benthic communities and identify seabed habitats most at risk from bottom trawling disturbance. However, the large variety of indicators and their development and application under specific geographic areas and management contexts has made it difficult to evaluate their wider utility. We compared the complementarity/uniqueness, sensitivity, and selectivity of 18 benthic indicators to pressure of bottom trawling. Seventeen common datasets with broad regional representation covering a range of pressure gradients from bottom trawling disturbance (n = 14), eutrophication (n = 1), marine pollution (n = 1), and oxygen depletion (n = 1) were used for the comparison. The outcomes of most indicators were correlated to a certain extent with response to bottom trawling disturbance, and two complementary groups of indicators were identified: diversity-based and biological trait-based indicators. Trait-based indicators that quantify the changes in relative abundance of sensitive taxa were most effective in identifying benthic community change in response to bottom trawling disturbance. None of the indicators responded to the trawling pressure gradient in all datasets, and some showed a response that were opposed to the theoretical expectation for some gradients. Indicators that showed clear responses to bottom trawling disturbance also showed clear responses in at least one other pressure gradient, suggesting those indicators are not pressure specific. These results emphasize the importance of selecting several indicators, at least one from each group (diversity and trait-based), to capture the broader signals of change in benthic communities due to bottom trawling activities. Our systematic approach offers the basis from which scientific advisors and/or managers can select suitable combinations of indicators to arrive at a sensitive and comprehensive benthic status assessment.

Rapid Analysis for α-Tocopherol and Its Oxidative Products in the Pisum sativum L. Leaf Using Supercritical Fluid Chromatography-Medium Vacuum Chemical Ionization Tandem Mass Spectrometry.

A method for the rapid determination of α-tocopherol (α-T) and its oxidative products in plant tissue has been developed using supercritical fluid extraction (SFE) coupled with supercritical fluid chromatography (SFC) and medium vacuum chemical ionization (MVCI) with tandem mass spectrometry. The method is designed to study changes in levels for α-T and its oxidative products in plant cells during photosynthesis, aiming to observe the light response curves. α-T oxidation is a non-enzymatic self-defense mechanism in plant cells. Unlike enzyme-involved reactions, it cannot be stopped, so the oxidation continues in crude extracts even after extraction. Therefore, a real-time in-situ method is essential for tracking the light response curves. To optimize the selective reaction monitoring method, the reaction mixture of α-T and singlet oxygen (1O2), generated by rose Bengal under light illumination, was used as the source of oxidative products. The relative abundance changes in α-tocopherylquinone and 8a-hydroperoxy tocopherone in Pisum sativum L. (Pea) leaves under excessive light illumination have been preliminarily analyzed as part of the light response curve study. The method archives a throughput of 10-15 minutes for analyzing duplicate leaf samples. This process includes cutting off the leaf, sectioning it, placing the sample in a frozen SFE vessel, and conducting SFE/SFC analysis. Consequently, the average throughput is approximately 5-7 minutes per sample.

Effects of Polyvinyl Chloride Microplastics on the Reproductive System, Intestinal Structure, and Microflora in Male and Female Mice

The pervasive use of plastics in numerous industrial sectors has resulted in the circulation of microplastics across diverse ecosystems and food chains, giving rise to mounting concerns regarding their potential adverse impacts on biological systems and the environment. The objective of this experiment was to investigate the distinct effects of microplastic-polyvinyl chloride (PVC) exposure on the reproductive system, intestinal tissue structure, and intestinal microbial flora of both male and female mice. A total of 24 4-week-old Kunming mice were randomly assigned to one of four groups: male control group (CM), female control group (CF), male PVC test group (PVCM), and female PVC test group (PVCF) (n = 6). The findings revealed that in terms of the reproductive system, the PVCM group exhibited an impaired testicular structure with an irregular arrangement and a significant reduction in spermatogonia, spermatocytes, and spermatozoa within the seminiferous tubules (p &lt; 0.01). The PVCF group exhibited a notable decrease in ovarian follicles (p &lt; 0.01), accompanied by a reduction in uterus volume, fallopian tube volume, and muscle layer thickness, all of which also decreased significantly (p &lt; 0.01). In comparison to the control groups, exposure to PVC resulted in a reduction in the width and height of the intestinal villi, accompanied by an increase in crypt depth. This led to a significant alteration in the ratio of villus height to crypt depth (V/C) (p &lt; 0.01). Moreover, a reduction in microbial species diversity was observed within both the PVCM and PVCF groups; additionally, it was accompanied by contrasting changes in relative abundance and functional gene profiles among the major intestinal flora constituents. In summary, the findings indicate that PVC induces damage to both male and female mice reproductive and digestive systems, further exhibiting notable sex-dependent effects on mouse intestinal microflora composition, which correlates significantly with its impact on reproductive organs.

Striped Field Mouse Invading Human-Modified Environments of Lithuania during Last Five Decades

The striped field mouse (Apodemus agrarius) is expanding in several European countries, but the details of this process are not always documented due to a lack of long-term studies. We conducted an analysis of changes in relative abundances and proportions of A. agrarius in small mammal communities in nine different habitat groups in Lithuania during 1975–2023. We found an increase in the abundance and proportion of A. agrarius, increasing synanthropization of the species, and tolerance to anthropogenization of habitats. Temporal variations in the relative abundance and proportion of species were observed, with lower values in February–July and higher values in September–January. The main finding is a remarkable increase in species presence in the country after the 1990s, with a peak observed in the 2010s–2020s, confirmed by eight local studies. During these decades, it was the third most abundant species, representing 19.8–20.0% of the individuals caught. It is also important to note that A. agrarius has recently been most abundant in commensal habitats (0.029 ± 0.006 individuals/trap day), with the highest species proportion in agricultural areas (24.8 ± 1.8%). There are many indications that the expansion of A. agrarius in Lithuania is becoming invasive.

Habitat type controls microarthropod community changes across a Magellanic sub-Antarctic elevation gradient

IntroductionElevation gradients are often used as a proxy for climate change as they allow comparisons of ecological responses over much larger temporal and spatial scales than is possible through experimental manipulations.MethodsHere, we tested how microarthropod communities (Collembola and Acari) are affected by climatic differences between sea level and 600 m a.s.l. on Navarino Island, in the Magellanic sub-Antarctic ecoregion of southern Chile (mean annual temperatures of 5.6 vs 3.1°C, respectively). We quantified microarthropod abundance, richness and community trait characteristics in dominant moss (Racomitrium lanuginosum and Polytrichum strictum) and lichen (Usnea trachycarpa, Pseudocyphellaria freycinetii and Stereocaulon alpinum) vegetation growing at both elevations. These moss and lichen genera are characterized by large morphological differences and allow testing of how habitat characteristics affect microarthropod community response across elevation gradients.ResultsCollembola and Acari community composition differed between the low and high elevation sites. Total abundance levels of Acari were maintained in each habitat across elevation, whereas Collembola richness strongly declined (50%) at high elevation in the moss habitats. Acari community differences across elevation were driven by relative abundance changes whereas the Collembola community lost species at higher elevation. An anticipated decline of smaller eudaphic Collembola at high elevation was only observed in the moss Racomitrium, reflecting potentially lower temperature buffering capacity and shelter options compared to Polytrichum. Lichens mostly supported larger epigeic species irrespective of elevation. There were no consistent patterns linking microarthropod communities with habitat water holding capacity or water loss rates across the studied habitats and elevation.DiscussionHabitat type and the genus of moss or lichen were associated with microarthropod community changes across elevation, including examples of declines, increases and no change. These findings highlight that community responses across gradients may not always relate to the generally hypothesized environmental variables (e.g. temperature variability) and that habitat characteristics should be taken into account when using elevation as a proxy for climate change.

Charting the Dynamic Trophoblast Plasma Membrane Identifies LYN As a Functional Regulator of Syncytialization.

The differentiation of placental cytotrophoblasts (CTBs) into the syncytiotrophoblast (STB) layer results in a significant remodeling of the plasma membrane proteome. Here, we use a peroxidase-catalyzed proximity labeling strategy to map the dynamic plasma membrane proteomes of CTBs and STBs. Coupled with mass-spectrometry-based proteomics, we identify hundreds of plasma membrane proteins and observe relative changes in protein abundance throughout differentiation, including the upregulation of the plasma-membrane-localized nonreceptor tyrosine kinase LYN. We show that both siRNA-mediated knockdown and small molecule inhibition of LYN kinase function impairs CTB fusion and reduces the expression of syncytialization markers, presenting a function for LYN outside of its canonical role in immunological signaling. Our results demonstrate the use of the proximity labeling platform to discover functional regulators within the plasma membrane and provide new avenues to regulate trophoblast differentiation.

PSX-15 Effect of starch supplementation on rumen bacterial abundance in Bos taurus indicus steers consuming low-quality forage

Abstract Deficient ruminally available nitrogen caused by a basal diet of low-quality forage can limit microbial growth in the rumen and decrease forage utilization. Protein supplementation is well-documented to improve forage digestibility and performance. Additionally, starch has been evaluated to increase energy supply to grazing cattle when the forage cannot support adequate levels of production. However, most research in this area has been conducted in Bos taurus taurus, especially the response of the rumen microbiome to supplementation. Accordingly, the objective of this study was to evaluate the effects of increasing starch supplementation on rumen bacterial populations in Bos taurus indicus steers supplemented protein and consuming low-quality forage. Ruminal samples were collected from five ruminally-cannulated Brahman steers (BW 420 ± 55 kg) used in a 4×4 Latin square fed a basal diet of King Ranch Bluestem Hay (3.5% CP and 73% NDF) provided ad libitum, and one of four isonitrogenous (130 mg N/kg BW) supplements with increasing levels of starch (2% starch= 100% soybean meal; 20% starch= 73% soybean meal, 26.2% corn, 0.8% urea; 38% starch = 47% soybean meal, 51.6% corn, 1.4% urea; 56% starch= 19% soybean meal, 78.6% corn, 2.4% urea). Rumen content samples were collected via rumen cannula at 4h post-feeding. Microbial DNA was extracted; full length 16S rRNA amplicon libraries were prepared using Kinnex kits and then sequenced on the PacBio Revio platform. Reads were analyzed using DADA2 and QIIME2. Statistical analysis was performed with the GLIMMIX procedure of SAS 9.4 (SAS Inst. Inc., Cary, NC). Firmicutes, Bacteroidata, Actinobacteriota, Verrucomicrobiota, and Euryarchaeota were the most abundant phyla in all treatments (83, 10, 3, 0.4, and 1%, respectively), and were not affected by treatment (P ≥ 0.10). Christensenellaceae R-7 group, Rikenellaceae RC9 gut group, Lachnospiraceae-XPB1014-group, Butyrvibrio, Lachnospiraceae-NK3A20-group, and Prevotella represented the most abundant genera for all treatments (7, 5, 11, 9, 7, and 3%, respectively). Lachnospiraceae-XPB1014-group and Lachnospiraceae-NK3A20-group responded quadratically (P ≤ 0.02) to increasing starch with decreased abundance for the 20% and 38% starch supplement. Comparatively, relative abundance of Butyrvibrio responded quadratically (P &amp;lt; 0.01) with increased abundance in the 20% and 38% starch supplement. Pseudobutyrvibrio increased with supplementation of 20% starch and then decreased as starch supplementation increased (quadratic, P = 0.04). In conclusion, supplementation of starch elicited changes in microbial relative abundance at the genus level with the response in Butyrivibrio suggesting greater fibrolytic activity. Forage and total digestible NDF intake in these steers decreased with increased starch supplementation; however, TDOMI was not affected by starch provision.

500 Effect of different iron sources on growth performance, gut health, and microbiota in nursery pigs

Abstract This study evaluated the effect of different iron sources, including iron polysaccharide complexes (SQM iron) and ferrous sulfate (FS) on growth performance, gut health, pathogenic bacteria load, colon fecal microbiota, and fecal iron concentration in nursery pigs. Nursery pigs (n = 320, TN70 cross, Topigs Norsvin Canada) weaned at 21 ± 2 d were randomly assigned to four treatments arranged in 2 x 2 factorial, with the factors being sanitation conditions (clean vs. dirty) and iron sources (SQM iron vs. FS, each at 100 mg iron/kg) to give 8 pens (10 piglets per pen) per treatment. Pigs were fed their respective diets in two phases over a 28-d period. Fecal scores, body weight (BW) and feed intake were recorded weekly. Iron content, gene expression of butyryl-CoA:acetate CoA-transferase and bisulfite reductase, and pathogenic bacteria counts were determined in fresh fecal samples collected on d 0, d 14, and d 21. On d 28, one pig randomly selected from each pen was euthanized to sample colon digesta for microbiota analysis and jejunal tissue and serum for gut integrity and permeability analysis. Data were analyzed using PROC MIXED of SAS followed by Tukey’s multiple comparison test except for raw 16s sRNA sequences, which were processed using QIIME2 and analyzed with Kruskal-Wallis test. Overall, from d 0 to14 SQM iron resulted in higher average daily gain (ADG) and average daily feed intake (ADFI; P &amp;lt; 0.05). SQM iron resulted in higher fecal iron at d 21 and improved fecal scores at d 27 (P &amp;lt; 0.05). SQM iron increased the relative abundance of fecal Campylobacter jejuni when comparing d 21 to d 0, and O157 E. Coli when comparing d 14 to d 0 (P &amp;lt; 0.05). Ferrous sulfate resulted in greater changes in relative abundance of butyryl-CoA:acetate CoA-transferase and bisulfate reductase than the SQM iron treatment under clean conditions when comparing d 21 to d 0 (P &amp;lt; 0.05). Dietary iron treatments did not significantly affect gastrointestinal integrity and permeability in jejunum and did not alter fecal microbiota composition on d 28. In conclusion, substituting 100 mg/kg added iron as FS with equal concentration of SQM iron improved ADG in the initial 2 wk and overall ADFI and promoted gut health indicators.

Lessons learned during a 12-year monitoring project with the endangered Magdalena River turtle (Podocnemis lewyana): hunting pressure, habitat degradation, and methodological considerations

Turtle species in the Family Podocnemididae, including the Colombian endemic and critically endangered Magdalena River Turtle Podocnemis lewyana, characteristically present low recapture rates that preclude estimation of population parameters using maximum likelihood modeling. In our 12-year monitoring project with this species, we evaluated changes in relative abundances, proportions of sex/size classes, and individual body sizes and body conditions in a population in four channels in the middle Magdalena River drainage. We also inspected for associations between trends in changes in these variables and differences in hunting pressure and habitat degradation. To inspect for temporal and spatial demographic dynamics, we estimated variation in relative abundances using the Catch Per Unit Effort index, the total number of turtles captured over an entire 5-day sampling period using ten baited funnel traps. Relative abundances and the proportions of sex/size classes were different between sites and years. We found a significant decline in the proportion of females and juveniles over time, along with evidence that the females still present were smaller in body size. Our results support the hypothesis that hunting eliminates adult females from these sites, perhaps also translating into a reduction in recruitment. The lack of evidence of generalized declines in body condition of all size classes suggests that habitat degradation might contribute less to the population declines in this region. Our results also illustrate that even when recapture rates are low, monitoring turtles via standardized trapping may yield insights into the population’s conservation status that other relative abundance indices cannot.

Dynamic interplay of immune response, metabolome, and microbiota in cows during high-grain feeding: insights from multi-omics analysis.

This study explores the dynamics of immune gene expression, ruminal metabolome, and gut microbiota in cows due to the duration of high-grain feeding, shedding light on host response and microbial dynamics in parallel. Cows consumed forage for a week, then gradually transitioned to a high-grain diet, which they consumed for 4 weeks. Immune response was evaluated in ruminal papillae by expression of genes related to the nuclear factor-kappaB (NFkB) pathway and correlated with the microbiota. Rumen metabolome was evaluated with high-performance liquid chromatography coupled with mass spectrometry and anion-exchange chromatography. Rumen and fecal microbiota were evaluated with 16S rRNA gene amplicon sequencing. In the rumen, expression of inflammation-associated genes increased with the duration on high grain, indicating activation of pro-inflammatory cascades; microbial diversity decreased with a high-grain diet but stabilized after week 3 on high grain. Changes in microbial relative abundance and metabolite enrichment were observed throughout the 4 weeks on high grain, with increments in propionogenic taxa (i.e., Succinivibrionaceae). Metabolite enrichment analysis showed that at the start of high-grain feeding, simple carbohydrates were enriched; then, these were substituted by their fermentation products. There were correlations between certain ruminal bacterial taxa (i.e., Ruminococcaceae UCG-005) and expression of genes of the NFkB pathway, suggesting the influence of these taxa on host immune response. In feces, microbial diversity and several Ruminococcaceae members initially declined but recovered by weeks 3 and 4. Overall, despite the stabilization of microbial diversity, changes in microbial relative abundance and proinflammatory genes were observed throughout high-grain feeding, suggesting that cows need more than 4 weeks to fully adjust once consuming a high-grain diet.IMPORTANCEDespite the stepwise diet transition typically assumed to serve for animal adaptation, expression of signaling receptors, mediators, and downstream targets of nuclear factor-kappaB pathway were found throughout the 4 weeks on high grain, which correlated with changes in the rumen microbial profile. In addition, although microbial diversity recovered in the feces and stabilized in the rumen in week 3 on high grain, we observed changes in microbial relative abundance throughout the 4 weeks on high grain, suggesting that cows need more than 4 weeks to adjust once consuming this diet. Findings are particularly important to consider when planning experiments involving dietary changes.

Proteomic profiling of Arabidopsis nuclei reveals distinct protein accumulation kinetics upon heat stress

Heat stress (HS) impacts the nuclear proteome and, subsequently, protein activities in different nuclear compartments. In Arabidopsis thaliana, a short exposure to 37 °C leads to loss of the standard tripartite architecture of the nucleolus, the most prominent nuclear substructure, and, consequently, affects the assembly of ribosomes. Here, we report a quantitative label-free LC‒MS/MS (Liquid Chromatography coupled to tandem Mass Spectrometry) analysis to determine the nuclear proteome of Arabidopsis at 22 °C, HS (37 °C for 4 and 24 h), and a recovery phase. This analysis identified ten distinct groups of proteins based on relative abundance changes in the nucleus before, during and after HS: Early, Late, Transient, Early Persistent, Late Persistent, Recovery, Early-Like, Late-Like, Transient-Like and Continuous Groups (EG, LG, TG, EPG, LPG, RG, ELG, LLG, TLG and CG, respectively). Interestingly, the RNA polymerase I subunit NRPA3 and other main nucleolar proteins, including NUCLEOLIN 1 and FIBRILLARIN 1 and 2, were detected in RG and CG, suggesting that plants require increased nucleolar activity and likely ribosome assembly to restore protein synthesis after HS.

The Effects of Aspirin Intervention on Inflammation-Associated Lingual Bacteria: A Pilot Study from a Randomized Clinical Trial.

Several bacterial taxa enriched in inflammatory bowel diseases and colorectal cancer (CRC) are found in the oral cavity. We conducted a pilot study nested within a six-week aspirin intervention in a randomized placebo-controlled trial to test their response to aspirin intervention. Fifty healthy subjects, 50-75 years old, were randomized to receive 325 mg aspirin (n = 30) or placebo (n = 20) orally once daily for six weeks. Oral tongue swabs were collected at baseline and week six. We estimated the association between aspirin use and the temporal changes in the relative abundance of pre-specified genus level taxa from pre- to post-treatment. The temporal change in relative abundance differed for eight genus level taxa between the aspirin and placebo groups. In the aspirin group, there were significant increases in the relative abundances of Neisseria, Streptococcus, Actinomyces, and Rothia and significant decreases in Prevotella, Veillonella, Fusobacterium, and Porphyromonas relative to placebo. The log ratio of Neisseria to Fusobacterium declined more in the aspirin group than placebo, signaling a potential marker associated with aspirin intervention. These preliminary findings should be validated using metagenomic sequencing and may guide future studies on the role of aspirin on taxa in various oral ecological niches.

Duodenal microbiota dysbiosis in functional dyspepsia and its potential role of the duodenal microbiota in gut-brain axis interaction: a systematic review.

Functional dyspepsia (FD) is a common gastrointestinal disorder associated with brain-gut interaction disturbances. In recent years, accumulating evidence points to the duodenum as a key integrator in dyspepsia symptom generation. Investigations into the pathological changes in the duodenum of FD patients have begun to focus on the role of duodenal microbiota dysbiosis. This review summarizes duodenal microbiota changes in FD patients and explores their relationship with gut-brain interaction dysregulation. Ten databases, including PubMed, MEDLINE, and the Cochrane Library, were searched from inception to 10th October 2023 for clinical interventional and observational studies comparing the duodenal microbiota of FD patients with controls. We extracted and qualitatively summarized the alpha diversity, beta diversity, microbiota composition, and dysbiosis-related factors. A total of nine studies, consisting of 391 FD patients and 132 non-FD controls, were included. The findings reveal that the alpha diversity of the duodenal microbiota in FD patients does not exhibit a significant difference compared to non-FD controls, although an upward trend is observed. Furthermore, alterations in the duodenal microbiota of FD patients are associated with the symptom burden, which, in turn, impacts their quality of life. In FD patients, a considerable number of duodenal microbiota demonstrate a marked ascending trend in relative abundance, including taxa such as the phylum Fusobacteria, the genera Alloprevotella, Corynebacterium, Peptostreptococcus, Staphylococcus, Clostridium, and Streptococcus. A more pronounced declining trend is observed in the populations of the genera Actinomyces, Gemella, Haemophilus, Megasphaera, Mogibacterium, and Selenomonas within FD patients. A negative correlation in the relative abundance changes between Streptococcus and Prevotella is identified, which correlates with the severity of symptom burden in FD patients. Moreover, the alterations in specific microbial communities in FD patients and their potential interactions with the gut-brain axis merit significant attention. Microbial dysbiosis in FD patients is linked to the onset and exacerbation of symptoms and is related to the disorder of gut-brain interaction. Larger-scale, higher-quality studies, along with comprehensive meta-omics research, are essential to further elucidate the characteristics of the duodenal microbiota in FD patients and its role in FD pathogenesis.Systematic review registration: CRD42023470279, URL: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023470279.

Relationship between Respiratory Microbiome and Systemic Inflammatory Markers in COPD: A Pilot Study.

The respiratory microbiome may influence the development and progression of COPD by modulating local immune and inflammatory events. We aimed to investigate whether relative changes in respiratory bacterial abundance are also associated with systemic inflammation, and explore their relationship with the main clinical COPD phenotypes. Multiplex analysis of inflammatory markers and transcript eosinophil-related markers were analyzed on peripheral blood in a cohort of stable COPD patients (n = 72). Respiratory microbiome composition was analyzed by 16S rRNA microbial sequencing on spontaneous sputum. Spearman correlations were applied to test the relationship between the microbiome composition and systemic inflammation. The concentration of the plasma IL-8 showed an inverted correlation with the relative abundance of 17 bacterial genera in the whole COPD cohort. COPD patients categorized as eosinophilic showed positive relationships with blood eosinophil markers and inversely correlated with the degree of airway obstruction and the number of exacerbations during the previous year. COPD patients categorized as frequent exacerbators were enriched with the bacterial genera Pseudomonas which, in turn, was positively associated with the severity of airflow limitation and the prior year's exacerbation history. The associative relationships of the sputum microbiome with the severity of the disease emphasize the relevance of the interaction between the respiratory microbiota and systemic inflammation.