Linear Discriminant Analysis Effect Size Research Articles

Immunoglobulin-coating patterns reveal altered humoral responses to gut bacteria in pediatric cow milk allergies.

Pediatric cow milk allergies (CMA) can occur in immunoglobulin (Ig) E and non-IgE-mediated forms. Unlike IgE-mediated allergies, the mechanisms of disease pathogenesis in non-IgE-mediated food allergy and an association with microbiome has not been well established. Previous studies have identified the presence of altered humoral responses to gut bacteria in IgE mediated allergies. Here, we analyzed IgA, IgE and IgG responses to gut bacteria in subjects with either IgE or non-IgE mediated CMA to identify relative proportions of Ig-coated bacteria and characterize unique disease specific microbial signatures. Multi-parametric flow cytometry analysis was used to identify IgA, IgE and IgG responses to gut bacteria in CMA patients. Cell sorting of Ig coated gut bacteria was subsequently performed followed by high throughput 16S rRNA gene sequencing and specific patterns of humoral responses to gut bacteria assessed in each study group. We identified significant alterations in IgA and IgG gut bacterial coating patterns in CMA subjects. Proportions of IgA-coated bacteria were decreased in IgE mediated CMA subjects without atopic dermatitis (ALL) and non-IgE mediated CMA subjects (ENP), compared to healthy controls (CON). In comparison, IgG-coated bacteria was significantly elevated in CMA subjects with atopic dermatitis (AD). Alpha and beta diversities displayed significant differences in IgA-, IgE-, and IgG-coated bacteria in AD and ENP groups. Significant differences in bacteria coated by IgA, IgE and IgG were detected at Phyla, Genus and Species levels and associated bacterial dysbiosis in IgE and non-IgE mediated allergies were identified. Linear discriminant analysis (LDA) effect size (LEFse) revealed unique disease associated bacterial signatures, including several pathogenic bacteria namely Bacteroides fragilis, Ruminococcus gnavus, Eubacterium dolichum, Fusobacterium, Clostridium neonatale and Robinsoniella peoriensis. Receiver operating characteristic curve analysis confirmed the efficiency of using the bacterial signatures identified as biomarkers for disease. Altered IgA and IgG responses to gut bacteria were identified in CMA subjects. The disease-specific responses were associated with alterations in bacterial diversity and concomitant dysbiosis of Ig-coated bacteria in IgE-mediated and non-IgE-mediated CMA pediatric subjects. The identification of pathogenic bacteria uniquely associated with different classes of allergic disease indicates a role of these bacteria in driving disease-specific pathological phenotypes.

Exploring the rumen microbial function in Angus bulls with divergent residual feed intake

This study leverages Shotgun metagenomics to assess the rumen microbial community and functionality in Angus bulls with differing residual feed intake-expected progeny difference (RFI-EPD) values, aiming to elucidate the microbial contributions to feed efficiency. Negative RFI-EPD bulls (NegRFI: n=10; RFI-EPD= -0.3883 kg/d) and positive RFI-EPD bulls (PosRFI: n=10; RFI-EPD=0.2935 kg/d) were selected from a group of 59 Angus bulls (average body weight (BW) = 428 ± 18.8 kg; 350 ± 13.4 d of age) fed a high-forage total mixed ration after a 60-d testing period. At the end of the 60-d period, rumen fluid samples were collected for bacterial DNA extraction and subsequent shotgun metagenomic sequencing. Results of the metagenome analysis revealed greater gene richness in NegRFI bulls, compared to PosRFI. Analysis of similarity revealed a small but noticeable difference (P =0.052; R-value = 0.097) in the rumen microbial community of NegRFI and PosRFI bulls. Linear Discriminant Analysis effect size (Lefse) was utilized to identify the differentially abundant taxa. The Lefse results showed that class Fibrobacteria (LDA = 5.1) and genus Fibrobacter (LDA = 4.8) were greater in NegRFI bulls, compared to PosRFI bulls. Relative abundance of the carbohydrate-active enzymes was also compared using Lefse. The results showed greater relative abundance of glycoside hydrolases and carbohydrate-binding modules such as GH5, CBM86, CBM35, GH43, and CBM6 (LDA > 3.0) in NegRFI bulls whereas GH13 and GT2 were greater in PosRFI bulls. The distinct metabolic and microbial profiles observed in NegRFI, compared to PosRFI bulls, characterized by greater gene richness and specific taxa such as Fibrobacter, and variations in carbohydrate-active enzymes, underscore the potential genetic and functional differences in their rumen microbiome. These findings contribute to a deeper understanding of the interplay between rumen microbiota and feed efficiency in Angus bulls, opening avenues for targeted interventions and advancements in livestock management practices.

Retraction: Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data.

The article Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data (10.3791/61715) has been retracted by the journal upon the authors' request due to a conflict regarding the data and methodology.

Comparative analysis of gut microbiota in incident and prevalent peritoneal dialysis patients with peritoneal fibrosis, correlations with peritoneal equilibration test data in the peritoneal fibrosis cohort.

The connection between peritoneal function and gut microbiota in peritoneal fibrosis (PF) patients remains uncertain. Peritoneal equilibration test (PET) was employed to evaluate peritoneal function in patients with peritoneal fibrosis (PF). 16S rRNA sequencing was used to analyze the gut flora in incident peritoneal dialysis (PD) and PF groups, identifying differential microbial communities. Spearman's correlation analysis, conducted using SPSS 26.0, was employed to explore the microbial associations with PF. In the PF group, the PET showed a 4-h dialysate-to-plasma creatinine ratio (D/PCr) ratio of 0.62 ± 1.01 and a 4-h ultrafiltration (UF) volume of 41.73 ± 76.71 mL with a 2.5% glucose dwell. The alpha diversity between the PD and PF groups did not exhibit a significant difference. The PD and PF groups were predominantly composed of Firmicutes, Tenericutes, and Ignavibacteriae. Linear discriminant analysis effect size (LEfse) analysis indicates that the Firmicutes, Lactobacillales, and Bacilli were significantly enriched in the PD group, whereas Lachnospiraceae, Phenylobacterium, and Caulobacteraceae were enriched among the PF group. The functional prediction of gut microbiota genes revealed variations in metabolic pathways related to lipid transport, energy metabolism, and post-translational protein modifications between the two cohorts. In the PF group, Ignavibacteriae and Bdellovibrio correlated positively with the 4-h D/PCr ratio (p <0.05), while Prevotella negatively correlated with the 4-h UF from 2.5% glucose dwell (p <0.05). The intestinal microbiota of patients newly initiated on peritoneal dialysis significantly differs from that of those with long-term peritoneal dialysis complicated by peritoneal fibrosis, with the latter's peritoneal function potentially linked to Prevotella, Ignavibacteriae, and Bdellovibrio.

Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.

Colorectal cancer (CRC) is one of the deadliest cancers worldwide, mostly arising from adenomatous polyps. Mounting evidence has demonstrated that changes in the gut microbiome play key roles in CRC progression, while quite few studies focused on the altered microbiota architecture of advanced adenoma (AA), a crucial precancerous stage of CRC. Thus, we aimed to investigate the microbial profiles of AA patients. Fecal samples were collected from 26 AA patients and 26 age- and sex-matched normal controls (NC), and analyzed by shotgun metagenomic sequencing. Gut microbial dysbiosis was observed in AA patients with lower alpha diversity. Advanced adenoma was characterized by an increased Bacillota/Bacteroidota ratio and higher Pseudomonadota levels compared to normal individuals. Linear discriminant analysis effect size (LEfSe) analysis was performed and identified 14 microbiota with significantly different abundance levels between AA and NC groups. Functional analysis revealed that tryptophan metabolism was upregulated in AA. Correspondingly, the expressions of gut microbes implicated in tryptophan metabolism also changed, including Akkermansia muciniphila, Bacteroides ovatus, Clostridium sporogenes, and Limosilactobacillus reuteri. The microbial network suggested that AA exhibited decreased correlation complexity, with Escherichia coli and Enterobacteriaceae unclassified harboring the strongest connectivity. A diagnostic model consisting of 3 microbial species was established based on random forest, yielding an area under the curve (AUC) of 0.799. Our study profiled the alterations of the gut microbiome in AA patients, which may enrich the knowledge of microbial signatures along with colorectal tumorigenesis and provide promising biomarkers for AA diagnosis.

Lactobacillus rhamnosus modulates murine neonatal gut microbiota and inflammation caused by pathogenic Escherichia coli

BackgroundPathogenic Escherichia coli strains produce neonatal septicemia after colonizing the neonatal gut. While the probiotic Lactobacillus rhamnosus GG (LGG) effectively reduces neonatal sepsis, LGG’s effects on the neonatal intestinal microbiota alterations and inflammation triggered by E. coli are incompletely understood. We hypothesized that LGG significantly modulates the specific neonatal gut microbial populations changes and the inflammatory response elicited by the enteral introduction of septicemia-producing E. coli. To test this hypothesis, newborn rats were pretreated orally with LGG or placebo prior to infection with the neonatal E. coli septicemia clinical isolate SCB34. Amplicon 16S rRNA gene sequencing was performed on intestinal samples. Intestinal injury and expression of inflammatory mediators and apoptosis were determined.ResultsAlpha diversity of gut microbiota was greater in SCB34-infected pups in comparison to sham-infected pups, these changes were not modified by LGG pretreatment. Beta diversity analyses also showed differences between SCB34-infected vs. uninfected pups. LGG pretreatment before SCB34 infection did not result in significant beta diversity changes compared to placebo. Moreover, individual genera and species abundance analyses by linear discriminant analysis effect size (LEfSe) showed significant changes in Gram-negative, Gram-positive, and anaerobic populations resulting from LGG pretreatment and SCB34 infection. LGG significantly suppressed the expression of inflammatory cytokines but did not attenuate SCB34-induced apoptosis or histologic injury.ConclusionsLGG modulates clinically significant microbiota features and inflammation triggered by pathogenic E. coli intestinal infection shortly after birth. This new knowledge can potentially be harnessed to design novel interventions against gut-derived neonatal sepsis.

Alterations in subgingival microbiome and advanced glycation end-products levels in periodontitis with and without type 1 diabetes mellitus: a cross-sectional study.

Existing studies predominantly focused on the relationship between periodontitis and type 2 diabetes mellitus (T2DM), with limited data on the association between periodontitis and type 1 diabetes mellitus (T1DM). This study aimed to examine the impact of T1DM and periodontitis on the subgingival microbiome and levels of advanced glycation end-products (AGEs). Samples were collected from four groups: T1DM, periodontitis (P), T1DM with periodontitis (DP), and periodontally and systemically healthy controls (Control). Subgingival microbiome composition and AGE levels were assessed using 16S rRNA gene sequencing and enzyme-linked immunosorbent assay (ELISA), respectively. Correlations between clinical indexes, microbiome composition, and AGEs were analyzed using Spearman correlation coefficient. Alpha and beta diversity analyses revealed significant differences in bacterial diversity between the DP group and other groups. Linear discriminant analysis effect size (LEfSe) analysis identified specific bacteria influencing each group: Acinetobacter, Leptotrichia, Raoultibacter, and Veillonella in the Control group; Tannerella, Porphyromonas, Filifactor, and Treponema in the P group; and Lactobacillales in T1DM individuals. Prevotella and Selenomonas were notably influential in the DP group. PICRUSt2 analysis showed pathways alterations were concentrated in cell motility, translation, cell growth and death and metabolism in the DP and P groups. Spearman correlation analysis indicated a positive correlation between AGEs and periodontitis or diabetes-related parameters and AGEs were positively correlated with Haemophilus and Arachnia. The findings suggested that the composition and function of the subgingival microbiome in the P group with or without T1DM were significantly different. Additionally, AGEs were involved in the development of periodontitis even in absence of hyperglycemia.

Vaginal microbiota in term pregnant women with differences in cervical ripeness revealed by 2bRAD-M

BackgroundCervical ripening is a multifactorial outcome, and the association between cervical ripening and vaginal microbiota remains unexplored in term primiparous women. A new sequencing technology, microbiome 2bRAD sequencing (2bRAD-M) that provides a higher level of species discrimination compared to amplicon sequencing. We applied 2bRAD-M to analyze the vaginal microbiota in a population with variations in cervical ripeness and to explore potential microbiota factors influencing cervical ripening.MethodsA total of 30 full-term primigravid women participated in this study, with 15 belonging to the low scoring group of cervical ripeness and 15 to the high scoring group. Clinical information was collected from the participants, and the vaginal microbiota and community structure of both groups were analyzed using 2bRAD-M sequencing. Microbiota diversity and differential analyses were conducted to explore potential factors influencing cervical ripening.ResultsA total of 605 species were detected. There was no difference in vaginal microbiota diversity between the two groups, and the vaginal microbial composition was structurally similar. In the two groups, Lactobacillus crispatus and Lactobacillus iners were identified as the two pivotal species through random forest analysis. Concurrent, extensive and close connections between species within the two groups were observed in the correlation analysis, influencing the aforementioned two species. Pairwise comparisons showed that Sphingomonas (P = 0.0017) and three others were abundant in high scoring group, while Alloprevotella (P = 0.0014), Tannerella (P = 0.0033), Bacteroides (P = 0.0132), Malassezia (P = 0.0296), Catonella (P = 0.0353) and Pseudomonas (P = 0.0353) and so on showed higher abundance in low scoring group. Linear discriminant analysis effect size identified 29 discriminative feature taxa.ConclusionFor the first time, vaginal microbiota was sequenced using 2bRAD-M. With a relatively simple structure, a more stable vaginal microbiota is associated with higher cervical ripeness, and certain microorganisms, such as Sphingomonas, may play a beneficial role in cervical ripening.

Effects of Helicobacter pylori and Helicobacter pylori eradication on the microbiota of tongue coating

Eradicating Helicobacter pylori (H. pylori) can cause an imbalance in the microbiota. Dysbiosis of the gut microbiome may produce multiple diseases and bacterial infections. The objective of this study was to investigate the influence of Helicobacter pylori (H. pylori) infection and its eradication on the composition of the oral tongue coating microbiota. A cohort of 35 participants was recruited and categorized into two groups: the H. pylori negative group (N group) consisting of 12 individuals and the H. pylori positive group (23 individuals). Within the H. pylori positive group, subjects were further stratified into the H. pylori pre-eradicated group (HPQ group) and the H. pylori eradicated group (HPH group). H. pylori positive individuals were treated with a quadruple regimen containing bismuth, and tongue coating samples were collected both prior to and following treatment. Concurrently, tongue coating samples were collected from H. pylori negative individuals. High-throughput 16S rRNA sequencing technology was employed to assess the microbial composition of the tongue coating in the N group, HPQ group, and HPH group. Pertinent clinical data were documented.Microbial diversity was found to significantly differ among the N group, HPQ group, and HPH group, as evidenced by variations in Chao1 index, Shannon index, and Partial Least Squares Discriminant Analysis (PLS-DA). The dominant bacterial phyla identified across all groups included Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria, and Saccharibacteria. At the phylum level, Firmicutes exhibited higher relative abundance in the HPQ group in comparison to both the N group and HPH group. Conversely, Bacteroidetes displayed greater prevalence in the N group and HPH group. Linear Discriminant Analysis Effect Size (LEfSe) analysis indicated a higher abundance of Romboutsia, Rothia, and Turiciactor in the HPQ group. Our study revealed significant disparities in microbial diversity and richness among the three groups. Furthermore, our findings suggest a potential association between the presence of Streptococcus, Rothia and H. pylori positive individuals.

Aggregatibacter is inversely associated with inflammatory mediators in sputa of patients with chronic airway diseases and reduces inflammation in vitro

BackgroundChronic airway disease (CAD) is characterized by chronic airway inflammation and colonization of the lungs by pro-inflammatory pathogens. However, while various other bacterial species are present in the lower airways, it is not fully understood how they influence inflammation. We aimed to identify novel anti-inflammatory species present in lower airway samples of patients with CAD.MethodsPaired sputum microbiome and inflammatory marker data of adults with CAD across three separate cohorts (Australian asthma and bronchiectasis, Scottish bronchiectasis) was analyzed using Linear discriminant analysis Effect Size (LEfSE) and Spearman correlation analysis to identify species associated with a low inflammatory profile in patients.ResultsWe identified the genus Aggregatibacter as more abundant in patients with lower levels of airway inflammatory markers in two CAD cohorts (Australian asthma and bronchiectasis). In addition, the relative abundance of Aggregatibacter was inversely correlated with sputum IL-8 (Australian bronchiectasis) and IL-1β levels (Australian asthma and bronchiectasis). Subsequent in vitro testing, using a physiologically relevant three-dimensional lung epithelial cell model, revealed that Aggregatibacter spp. (i.e. A. actinomycetemcomitans, A. aphrophilus) and their cell-free supernatant exerted anti-inflammatory activity without influencing host cell viability.ConclusionsThese findings suggest that Aggregatibacter spp. might act to reduce airway inflammation in CAD patients.

An innovative technology for producing agricultural Jiaosu from fruit waste without additional sugar and water: Fermentation characteristics, microbial community, and its impact on the growth of pakchoi

Landfilling or incineration of fruit waste causes serious environmental problems and economic losses. Agricultural Jiaosu (AJ) can convert fruit waste into agricultural inputs. However, traditional AJ preparation requires large amounts of brown sugar and water, restricting its large-scale application. In this study, five types of single fruit waste and one type of mixed fruit waste were used to produce AJ without additional of sugar and water. The physicochemical properties and microbial community dynamics of AJ fermentation were analyzed, and the effects and potential mechanism of AJ in promoting pakchoi growth were evaluated. The results showed that during the digestion process, the pH value of all AJ gradually decreased to below 3.6. Organic acids were the main metabolites, lactic acid and acetic acid accounted for 46.55 %–99.22 % of all organic acids. As fermentation progressed, Firmicutes gradually replaced Proteobacteria as the most dominant phylum, accounting for 54.1 %–99.41 % of the microbial communities. After 90 days, Lactobacillus and Lentilactobacillus were the dominant genera in all AJ, accounting for 44.49 %–92.54 % of the communities. Structural equation modeling revealed that AJ promoted plant growth through organic acids and bacterial community. This study is the first time to propose the concept of producing AJ from fruit waste without additional sugar and water and reveals the fermentation characteristics and microbial dynamics of AJ, as well as its potential mechanism as a biological inoculant in promoting plant growth. This study provides a new approach for the large-scale utilization of fruit waste to produce green agricultural inputs.Abbreviations: AJ, agricultural Jiaosu; ANOVA, analysis of variance; ASVs, amplicon sequence variants; DNA, deoxyribonucleic acid; HPLC, high performance liquid chromatography; LDA, linear discriminant analysis; LEfSe, linear discriminant analysis effect size; PCoA, Principal coordinates analysis; PCR, polymerase chain reaction; RDA, redundancy analysis; rRNA, ribosomal RNA; SEM, structural equation modeling.

Fungal communities in three root herbs: Insights and implications

The roots of Astragali Radix (AM), Dioscoreae Rhizome (DR), and Codonopsis Radix (CR) are frequently used in classical tonic formulations and dietary supplements. Given the extended exposure of rhizomes to complex biological environments, it is necessary to investigate the fungal composition of their surface. In this study, the fungal communities in the three root herbs were analyzed by DNA metabarcoding, and an extensive comparison of the fungal diversity at each taxonomic level was carried out. Furthermore, we examined the effects of species, collection site, and processing method on the fungal community. In Astragali Radix and Codonopsis Radix samples, Cladosporium was the predominant genus, with relative abundances of 1.98 %-76.81 % and 1.69 %-85.59 %, respectively. Aspergillus (0.08 %–99.92 %) was the prevailing genus in Dioscoreae Rhizome samples. Meanwhile, a total of 12 potential toxigenic fungi were identified, including Aspergillus restrictus, Fusarium oxysporum, and Penicillium citrinum. Moreover, the variations in fungal diversity and community composition from different collection sites and processing approaches were observed. Linear discriminant analysis effect size indicated significant differences in the relative abundance of genera among the three root herbs. Gibberella and Mucor genera were significantly enriched in Astragali Radix samples, while Yarrowia and Cladosporium genera exhibited significant enrichment in Dioscoreae Rhizome and Codonopsis Radix samples, respectively (p≤0.001). This study presents novel insights into the fungal profiles of three root herbs, thereby providing references for their safe utilization and quality improvement.

Divergence of rhizosphere microbial communities between females and males of the dioecious Hippophae tibetana at different habitats.

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, little is known about the difference in rhizosphere microbes in dioecious plants. In this study, we used amplicon sequencing to analyze the differences in rhizosphere microbial diversity and community composition of males and females of dioecious Hippophae tibetana at different habitats, and their key factors in driving the differences were investigated. The results showed that there were differences in the diversity, community composition, and connectivity and complexity of the co-occurrence network of rhizosphere microbes between females and males of the dioecious H. tibetana at different habitats. Zoopagomycota is a unique phylum of rhizosphere fungi in the males of the dioecious H. tibetana, while Dependentiae is a unique phylum of rhizosphere bacteria in the females of the dioecious H. tibetana. Linear discriminant analysis effect size (LEfSe) analysis indicated significant enrichment of species at different levels, suggesting that these species could be potential biomarkers for females and males of H. tibetana. Spearman's analysis showed that the dominant genera of rhizosphere fungi were significantly positively correlated with soil physicochemical properties (total nitrogen and phosphorus; organic matter; available phosphorus, potassium and nitrogen; salt content; water content). PICRUSt and FUNGuild predictive analysis indicated that the function of rhizosphere fungi was different between females and males of the dioecious H. tibetana at different habitats, while metabolites were the dominant functions of rhizosphere bacteria in all samples. These results highlighted the sexual discrimination of rhizosphere microbes on the dioecious plants and provided important knowledge for females and males of the dioecious plant-microbe interaction.IMPORTANCEThis study explores the differences in rhizosphere microbes of dioecious Hippophae tibetana at different habitats and their key factors in driving the differences. Through employing amplicon sequencing techniques, we found that rhizosphere microbial communities and diversity were different between females and males of the dioecious H. tibetana at different habitats, and there notably existed unique phylum and potential biomarkers of rhizosphere microbes between females and males of the dioecious H. tibetana. Rhizosphere fungi were significantly positively correlated with soil physicochemical properties. This study reveals the differences in rhizosphere microbes of dioecious H. tibetana at different habitats and driving factors; it also contributes to our understanding of the dioecious plant-microbe interaction.

Gut microbiota as a prognostic biomarker for unresectable hepatocellular carcinoma treated with anti-PD-1 therapy.

To investigate the relationship between the gut microbiome and the response to anti-PD-1-based combination therapy in unresectable hepatocellular carcinoma (HCC). We aimed to identify potential non-invasive biomarkers and new strategies to modulate immunotherapy in HCC. In this study, fresh stool samples and clinical data were collected from unresectable HCC patients treated with anti-PD-1-based combination therapy at the Cancer Hospital of the Chinese Academy of Medical Sciences between January 2020 and December 2021. The patients were divided into two groups based on their response to treatment: the treatment responder group (R group) and the treatment non-responder group (NR group). The composition and diversity of the gut microbiome were bioinformatically analyzed by using the Whole Genome Shotgun strategy, including taxonomic composition analysis, Alpha diversity analysis, Beta diversity analysis, and differentially enriched bacterial taxa analysis. Differentially enriched bacterial taxa between R and NR groups were identified based on the magnitude of the linear discriminant analysis effect size (LEfSe) and analyzed for their impact on the survival of the patient. A total of 45 eligible patients with unresectable HCC treated with anti-PD-1-based combination therapy participated in this study. The gut microbiological composition and Alpha diversity of patients were not statistically different, but there was a statistically significant difference in Beta diversity between the R and NR groups. (PERMANOVA tests, P = 0.006). We further identified 56 enriched bacterial taxa in the R group and 44 enriched bacterial taxa in the NR group based on the LEfSe analysis (LDA >2.66, P< 0.05). Patients with a high abundance of Collinsella genus, Ruminococcus_AM4211, and Ruminococcus_AF25_28AC had a longer median PFS and median OS compared to those with low abundance (P < 0.05). On the contrary, the median PFS and OS of patients with a high abundance of Bacteroides_AF20_13LB and Veillonella_atypica were significantly shorter than those of patients with low abundance (P < 0.05). The multivariate analysis showed that the abundance of Bacteroides_AF20_13LB and Ruminococcus_ AF25_28AC was independent related factors for PFS, and the abundance of Bacteroides_AF20_13LB was an independent related factor of OS. The enrichment of specific gut microbiota affected clinical efficacy and survival benefits in HCC treated with anti-PD-1 therapy and may be a promising non-invasive gut microbial biomarker and a new strategy for modulating immunotherapy in HCC.

The effects of AG1® supplementation on the gut microbiome of healthy adults: a randomized, double-blind, placebo-controlled clinical trial.

This study aimed to examine the effect of a commercially available multi-ingredient powder (AG1Ⓡ) on the gut microbiome and assess the impact of AG1Ⓡ on GI tolerability and other clinical safety markers in healthy men and women. Using a double-blind, randomized, two-arm, placebo-controlled, parallel design, we examined a 4-week daily supplementation regimen of AG1Ⓡ vs. placebo (PL). Fifteen men and 15 women provided stool samples for microbiome analysis, questionnaires for digestive quality of life (DQLQ), and completed visual analog scales (VAS) and Bristol stool charts to assess stool consistency and bowel frequency before and after the 4-week intervention. Participant's blood work (CBC, CMP, and lipid panel) was also assessed before and after the 4-week intervention. Alpha diversity was determined by Shannon and Chao1 index scores and evaluated by a two-way ANOVA, beta diversity in taxonomic abundances and functional pathways was visualized using partial least squares-discriminant analyses and statistically evaluated by PERMANOVA. To identify key biomarkers, specific feature differences in taxonomic relative abundance and normalized functional pathway counts were analyzed by linear discriminant analysis (LDA) effect size (LEfSe). Questionnaires, clinical safety markers, and hemodynamics were evaluated by mixed factorial ANOVAs with repeated measures. This study was registered on clinicaltrials.gov (NCT06181214). AG1Ⓡ supplementation enriched two probiotic taxa (Lactobacillus acidophilus and Bifidobacterium bifidum) that likely stem from the probiotics species that exist in the product, as well as L. lactis CH_LC01 and Acetatifactor sp900066565 ASM1486575v1 while reducing Clostridium sp000435835. Regarding community function, AG1Ⓡ showed an enrichment of two functional pathways while diminishing none. Alternatively, the PL enriched six, but diminished five functional pathways. Neither treatment negatively impacted the digestive quality of life via DQLQ, bowel frequency via VAS, or stool consistency via VAS and Bristol. However, there may have been a greater improvement in the DQLQ score (+62.5%, p = 0.058, d = 0.73) after four weeks of AG1Ⓡ supplementation compared to a reduction (-50%) in PL. Furthermore, AG1Ⓡ did not significantly alter clinical safety markers following supplementation providing evidence for its safety profile. AG1Ⓡ can be consumed safely by healthy adults over four weeks with a potential beneficial impact in their digestive symptom quality of life.

Oral Microbiota Variations in Psoriasis Patients Without Comorbidity.

Psoriasis is a chronic inflammatory skin disease, and its etiology is still unclear. There is increasing evidence suggesting that microorganisms may trigger psoriasis. However, the relationship between psoriasis and oral microbiota remains poorly understood. Our aim is to identify differences in the composition and diversity of the oral microbiota between patients with psoriasis and healthy controls, and to discover oral microbial markers for assessing the severity of psoriasis. This study recruited 20 psoriasis patients and 20healthy individuals, collecting their saliva to analyze the composition of the oral microbiota in psoriasis patients. We employed 16S rRNA sequencing technology and utilized various methods for oral microbiome analysis, including the Shannon Index, Gini-Simpson Index, Principal Coordinates Analysis (PCoA), non-metric multidimensional scaling (NMDS), Linear discriminant analysis Effect Size (LEfSe), Wilcoxon test, and Spearman's rank correlation. The results showed that the alpha diversity of oral microbiota was higher in psoriasis patients. The relative abundances of certain bacterial taxa differed between psoriasis and healthy individuals, including Prevotella, Prevotella 7 and Porphyromonas gingivalis, which are increased in psoriasis. We also found a positive correlation between Alloprevotella, Porphyromonas, and Neisseria with the severity of psoriasis, while Veillonella showed a negative correlation. In summary, this study found significant changes in the composition of the oral microbiota in patients with psoriasis. Some oral bacteria are associated with psoriasis severity. It provides a new perspective on the relationship between the oral microbiota and psoriasis.

Carvacrol acts on the larval midgut of Spodoptera frugiperda by destroying the tissue structure and altering the bacterial community

The fall armyworm, Spodoptera frugiperda, has become a global invasive pest in recent years, threatening agricultural production. Carvacrol (CAR) is a multifunctional plant-derived compound and exhibited significant bioactivities against many pests. Our previous study found that CAR inhibited growth and development in S. frugiperda. However, the effects of CAR on the midgut of this pest remain unknown. In this study, the actions of CAR on the larval midgut of S. frugiperda were investigated. The results found that 1.0 and 2.0 g/kg CAR treatments destroyed the structure of the larval midgut based on hematoxylin-eosin staining and transmission electron microscope observation. In addition, 2.0 g/kg CAR exposure significantly altered the larval midgut bacterial community composition and structure. The results of the linear discriminant analysis effect size (LEfSe) analysis suggest that six bacterial genera contributed to the different structures of the larval bacterial community. Furthermore, PICRUSt2 analysis found that 16 bacterial function categories were altered by CAR treatment, of which 8 were significantly increased. Our results provided new insight into the toxicological mechanisms of CAR against S. frugiperda larvae and laid the foundation for the field application of S. frugiperda control.

Integrating fecal metabolomics and gut microbiome to reveal the mechanism of Schisandra chinensis-Acorus tatarinowii Schott treatment in Alzheimer’s disease rats

BackgroundSchisandra chinensis (Turcz.) Baill (Schisandraceae) and Acorus tatarinowii Schott (Araceae Juss) (Sc-At) are two traditional Chinese medicinal herbs that are widely used in the treatment of neurological disorders such as insomnia. In our previous study, we found that Sc-At could improve the therapeutic efficacy of Alzheimer’s disease by affecting aromatase activity and estrogen levels, among other pathways. Material and methodsIn this study, first, the ameliorative effect of Sc-At on cognitive dysfunction in Alzheimer’s disease model rats was verified by Y-maze test together with Elisa assay. Second, fecal untargeted metabolomics analysis was performed using a UPLC-Q-TOF/MS-based metabolomics approach. 16S rDNA sequencing was utilized to screen the differential flora between groups, and linear discriminantan alysis effect size (LEfSe) was used to find the target flora. Finally, Spearman correlation analysis was combined to find the relationship between differential flora and differential metabolites in feces. Results(1) The results of Y-maze test and Elisa assay indicated that Sc-At could improve the cognitive dysfunction of AD model rats. (2) Metabolomics results showed that fecal metabolite levels were significantly different from those of rats in the blank group, and 18 potential biomarkers in feces were screened, mainly affecting linoleic acid metabolism, steroid hormone biosynthesis, sphingomyelin metabolism, riboflavin metabolism, etc. The 16S rDNA results showed that the abundance and diversity of intestinal flora in AD rats were destroyed, and the Sc-At treatment was able to reverse these changes. (3) Spearman’s correlation analysis showed a significant correlation between differential metabolites in feces and intestinal flora, further suggesting that Sc-At treats Alzheimer’s disease through the gut-brain axis. ConclusionsIn this study, we explored the mechanism of Sc-At in the treatment of Alzheimer’s disease by integrating fecal untargeted metabolomics and 16S rDNA gene sequencing, and the results showed that Sc-At exerts therapeutic effects on Alzheimer’s disease by improving the intestinal flora and related metabolic pathways.

Higher Microbial Abundance and Diversity in Bronchus-Associated Lymphoid Tissue (BALT) Lymphomas than in Non-Cancerous Lung Tissues.

It is well known that the majority of the extranodal marginal zone lymphomas of mucosa-associated lymphoid tissues (MALT lymphomas) are associated with microbiota, e.g., gastric MALT lymphoma with Helicobacter pylori. In general, they are very sensitive to low-dose radiotherapy and chemotherapeutic agents. The microbiota profile is not clearly elucidated in bronchus-associated lymphoid tissue (BALT) lymphoma, a rare type of MALT lymphoma in the lung. Thus, this study aimed to clarify the intratumor microbiome in BALT lymphoma using the third-generation NGS method. DNAs were extracted from 12 formalin-fixed paraffin-embedded (FFPE) tumor tissues obtained from BALT lymphoma patients diagnosed between 1990 and 2016. 16S rRNA gene was amplified by polymerase chain reaction. Amplicons were sequenced using a Nanopore platform. Next-generation sequencing analysis was performed to assess microbial profiles. For comparison, FFPE specimens from nine non-cancerous lung tissues were also analyzed. Specific bacterial families including Burkholderiaceae, Bacillaceae, and Microbacteriaceae were associated with BALT lymphoma by a linear discriminant analysis effect size approach. Although the number of specimens was limited, BALT lymphomas exhibited significantly higher microbial abundance and diversity with distinct microbial composition patterns and correlation networks than non-cancerous lung tissues. This study provides the first insight into intratumor microbiome in BALT lymphoma using the third-generation NGS method. A distinct microbial composition suggests the presence of a unique tumor microenvironment of BALT lymphoma.

Effects of progesterone administered to maternal rats during the teratogenesis-sensitive period through different routes on neurobehavior and gut microbiota in offspring

Objective: Progesterone (P4) is the optimal agent for luteal support in assisted reproductive technologies. Despite the availability of various formulations, the impacts of P4 treatment administered through different routes on offspring growth remain unevaluated. This study aimed to investigate and compare the effects of P4 administration through three different routes in pregnant rats during the teratogenesis-sensitive period on fertility outcomes and the behavior, plasma P4 and pregnenolone levels, and alterations in gut microbiota in the filial generation (F1) of offspring. Methods: Female rats that mated successfully were randomly classified into four groups: Group 1, the normal control group; Group 2, the IG group, in which utrogestan was administered via intragastric gavage; Group 3, the IM group, in which P4 was administered via intramuscular injection; and Group 4, the VAGIN group, in which P4 sustained-release vaginal gel was administered through the vagina. Except for the control group, P4 was administered in other groups through their respective routes for 13 consecutive days daily during the teratogenic-sensitive gestation period (days 6–18). The fertility outcomes of the maternal rats were observed, and open-field and three-chamber social preference tests were conducted to assess anxiety and social behavior, along with an exhaustive swimming experiment to evaluate the motor endurance of the offspring. Plasma P4 and pregnenolone levels in the offspring were measured, and fecal samples were assessed using gut microbiota sequencing and subsequent bioinformatics analysis. Results: No significant alterations in fertility outcomes were observed through three P4 administration routes—intragastric gavage, intramuscular injection, and vaginal administration—in rats. However, in behavioral experiments in offspring, a significant increase was observed in swimming time in the IG group than in the control group (P = 0.013). Furthermore, the offspring in the IG group exhibited a marked decrease in non-social behaviors compared with the control group (P = 0.030). No significant behavioral changes were observed in the F1 offspring in the open-field test. Additionally, the offspring in the IG group exhibited a significant elevation in plasma pregnenolone levels compared with the control group (P = 0.019) 30 days after birth. No notable differences in the α-diversity of gut microbiota were observed among the groups. However, significant differences in β-diversity were observed in both the IG and IM groups compared with the control group, indicating that P4 treatment via the two routes exhibited a significant impact on the gut microbiota composition of F1 offspring. Distinct differences were observed in the gut microbiota of the offspring among the three P4 treatment groups, with 22, 28, and 33 differential bacterial taxa identified in the IG, IM, and VAGIN groups, respectively, using linear discriminant effect size analysis, whereas Olivella appeared exclusively in the control group rather than in the P4 treatment groups. Conclusion: Oral administration of P4 to maternal rats during the teratogenesis-sensitive period enhanced motor endurance and plasma pregnenolone levels and altered the composition of the gut microbiota in the offspring. Our findings demonstrated different effects on offspring growth when P4 is administered orally, intramuscularly, or vaginally.