Linear Discriminant Effect Size Research Articles

Prediction and causal inference of hyperuricemia using gut microbiota.

Hyperuricemia (HUA) is a symptom of high blood uric acid (UA) levels, which causes disorders such as gout and renal urinary calculus. Prolonged HUA is often associated with hypertension, atherosclerosis, diabetes mellitus, and chronic kidney disease. Studies have shown that gut microbiota (GM) affect these chronic diseases. This study aimed to determine the relationship between HUA and GM. The microbiome of 224 men and 254 women aged 40years was analyzed through next-generation sequencing and machine learning. We obtained GM data through 16S rRNA-based sequencing of the fecal samples, finding that alpha-diversity by Shannon index was significantly low in the HUA group. Linear discriminant effect size analysis detected a high abundance of the genera Collinsella and Faecalibacterium in the HUA and non-HUA groups. Based on light gradient boosting machine learning, we propose that HUA can be predicted with high AUC using four clinical characteristics and the relative abundance of nine bacterial genera, including Collinsella and Dorea. In addition, analysis of causal relationships using a direct linear non-Gaussian acyclic model indicated a positive effect of the relative abundance of the genus Collinsella on blood UA levels. Our results suggest abundant Collinsella in the gut can increase blood UA levels.

Characteristics of gut microbiota and its correlation with hs-CRP and somatic symptoms in first-episode treatment-naive major depressive disorder

ObjectiveMost patients with major depressive disorder (MDD) have somatic symptoms, but little studies pay attention in the microbial-inflammatory mechanisms of these somatic symptoms. Our study aimed to investigate alterations in gut microbiota and its correlation with inflammatory marker levels and somatic symptoms in first-episode treatment-naive MDD. MethodsSubjects contained 160 MDD patients and 101 healthy controls (HCs). MDD patients were divided into MDD with somatic symptoms group (MDDS) and MDD without somatic symptoms group (MDDN) based on Somatic Self-rating Scale (SSS). 16S ribosomal RNA sequencing were performed to analyze the composition of the fecal microbiota. The inflammatory factors were measured using enzyme linked immunosorbent assay (ELISA). Correlation among the altered gut microbiota, inflammatory factor and severity of clinical symptoms were analysized. ResultsRelative to HCs, MDD patients had higher levels of high-sensitivity C-reactive protein (hs-CRP) as well as disordered α-diversity and β-diversity of gut microbiota. Linear discriminant effect size (LEfSe) analysis showed that MDD patients had higher proportions of Bifidobacterium, Blautia, Haemophilus and lower proportions of Bacteroides, Faecalibacterium, Roseburia, Dialister, Sutterella, Parabacteroides, Bordetella, and Phascolarctobacterium from the genus aspect. Furthermore, correlation analysis showed Bacteroides and Roseburia had negative correlations with the hs-CRP, HAMD-24, the total and factor scores of SSS in all participants. Further, compared with MDDN, the Pielous evenness was higher in MDDS. Random Forest (RF) analysis showed 20 most important genera discriminating MDD-S and MDDN, HCs. The ROC analysis showed that the AUC was 0.90 and 0.81 combining these genera respectively. ConclusionOur study manifested MDD patients showed disordered gut microbiota and elevated hs-CRP levels, and altered gut microbiota was closely associated with hs-CRP, depressive symptoms, and somatic symptoms.

Metagenetic analysis of the bacterial diversity of Kazakh koumiss and assessment of its anti-Candida albicans activity.

Koumiss, a five-thousand-year-old fermented mare's milk beverage, is widely recognized for its beneficial nutrient and medicinal properties. The microbiota of Chinese and Mongolian koumiss have been largely characterized in recent years, but little is known concerning Kazakh koumiss despite this drink historically originates from the modern Kazakhstan territory. In addition, while koumiss is regarded as a drink with therapeutic potential, there are also no data on koumiss anti-Candida activity. In this context, the aims of the present study were to investigate the bacterial diversity and anti-Candida albicans activity of homemade Kazakh koumiss samples as well as fermented whey and cow's milk, derived from koumiss and propagated for several months. Koumiss bacterial communities were largely dominated by lactic acid bacteria including Lactobacillus sensu lato spp. (69% of total reads), Streptococcus (8.0%) and Lactococcus (6.1%), while other subdominant genera included Acetobacter (2.6%), Enterobacter (2.4%), and Klebsiella (1.5%). Several but not all koumiss samples as well as fermented whey and cow's milk showed antagonistic activities towards C. albicans. Linear discriminant effect size (LEfSe) analysis showed that their bacterial communities were characterized by a significantly higher abundance of amplicon sequence variants (ASV) belonging to the genus Acetobacter. In conclusion, this study allowed to identify the key microorganisms of Kazakh koumiss and provided new information on the possible underestimated contribution of acetic acid bacteria to its probiotic properties.

Analysis of differences in intestinal flora associated with different BMI status in colorectal cancer patients

BackgroundOverweight is known to be an important risk factor for colorectal cancer (CRC), and the differences in intestinal flora among CRC patients with different BMI status have not been clearly defined. The purpose of this study was to elucidate the differences in the abundance, composition and biological function of intestinal flora in CRC patients with different BMI status.MethodA total of 170 CRC patients were included and grouped according to the BMI data of CRC patients. BMI ≥ 24 kg/m2 was defined as overweight group, and BMI within the range of 18.5–23.9 kg/m2 was defined as normal weight group. Preoperative stool collection of patients in both groups was used for 16S rRNA sequencing. Total RNA was extracted from 17 CRC tumor tissue samples for transcriptome sequencing, and then CIBERSORT algorithm was used to convert the transcriptome data into the relative content matrix of 22 kinds of immune cells, and the correlation between different intestinal flora and immune cells and immune-related genes under different BMI states was analyzed. Finally, we identified BMI-related differential functional pathways and analyzed the correlation between these pathways and differential intestinal flora.ResultThere was no significant difference in α diversity and β diversity analysis between overweight group and normal weight group. Partial least square discriminant analysis (PLS-DA) could divide the flora into two different clusters according to BMI stratification. A total of 33 BMI-related differential flora were identified by linear discriminant effect size analysis (LEfSe), among which Actinomyces, Desulfovibrio and Bacteroides were significantly enriched in overweight group. ko00514: Other types of O-glycan biosynthesis are significantly enriched in overweight group. There was a significant positive correlation between Clostridium IV and Macrophages M2 and T cells regulatory (Tregs). There was a significant negative correlation with Dendritic cells activated and T cells CD4 memory activated.ConclusionsThe richness and diversity of intestinal flora of CRC patients may be related to different BMI status, and the enrichment of Actinomyces, Desulphurvibrio and Bacteroides may be related to overweight status of CRC patients. The tumor microenvironment in which BMI-related differential flora resides has different immune landscapes, suggesting that some intestinal flora may affect the biological process of CRC by regulating immune cell infiltration and immune gene expression, but further experiments are needed to confirm this.

Maternal Exposure to Endocrine-Disrupting Chemicals: Analysis of Their Impact on Infant Gut Microbiota Composition.

Endocrine disruptors (EDCs) are chemicals that interfere with the endocrine system. EDC exposure may contribute to the development of obesity, type 2 diabetes, and cardiovascular diseases by impacting the composition of an infant's gut microbiota during the first 1000 days of life. To explore the relationship between maternal urinary levels of Bisphenol-A and phthalates (UHPLC-MS/MS), and the composition of the infant gut microbiota (16S rDNA) at age 12 months (T3) and, retrospectively, at birth (T0), 1 month (T1), and 6 months (T2), stool samples from 20 infants breastfed at least once a day were analyzed. Metataxonomic bacteria relative abundances were correlated with EDC values. Based on median Bisphenol-A levels, infants were assigned to the over-exposed group (O, n = 8) and the low-exposed group (B, n = 12). The B-group exhibited higher gut colonization of the Ruminococcus torques group genus and the O-group showed higher abundances of Erysipelatoclostridium and Bifidobacterium breve. Additionally, infants were stratified as high-risk (HR, n = 12) or low-risk (LR, n = 8) exposure to phthalates, based on the presence of at least three phthalates with concentrations exceeding the cohort median values; no differences were observed in gut microbiota composition. A retrospective analysis of gut microbiota (T0-T2) revealed a disparity in β-diversity between the O-group and the B-group. Considering T0-T3, the Linear Discriminant Effect Size indicated differences in certain microbes between the O-group vs. the B-group and the HR-group vs. the LR-group. Our findings support the potential role of microbial communities as biomarkers for high EDC exposure levels. Nevertheless, further investigations are required to deeply investigate this issue.

Population-level prokaryotic community structures associated with ferromanganese nodules in the Clarion-Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing.

Although deep-sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule-associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)-level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species-level monitoring might have overlooked nodule-specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion-Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV-level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule-surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat-specific. We identified 178 nodule-associated ASVs and 41 ASVs associated with nodule-surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule-specific ASVs are promising targets for future investigation of the nodule formation process.

The preliminary evidence on the association of the gut microbiota with stroke risk stratification in South Chinese population.

This study aimed to investigate the association between the gut microbiota and the risk of stroke. Faecal samples from 60 participants in South China, including 45 individuals with risk factors for stroke and 15 healthy controls, were collected and subjected to 16S rRNA sequencing. A bioinformatics analysis was performed to characterise the gut microbial diversity and taxonomic compositions at different risk levels (low, moderate, and high) of stroke. Functional prediction and correlation analyses between the microbiota and laboratory markers were performed to explore the potential mechanisms. A significant difference in beta diversity was observed between the participants from the stroke risk and healthy control groups. Linear discriminant effect size analysis revealed a large number of vascular beneficial bacteria enriched in the participants from the healthy control and low-risk groups, but a few vascular harmful bacteria were more abundant in the participants from the high-risk group than in those from the other groups. In addition, Anaerostipes, Clostridium_XlVb, and Flavonifractor, all of which belonged to the Firmicutes phylum, were enriched in the participants from the low-risk group, and their relative abundances gradually decreased as the stroke risk increased. Spearman's analysis revealed that these outstanding microbiota correlated with the levels of triglycerides, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, white blood cells, neutrophils, and carotid intima-media thickness. The preliminary evidence suggests that gut microbiota is associated with stroke risk. It potentially ameliorates atherosclerosis by targeting lipid metabolism and inflammation. This provides novel insights into the early screening of stroke risk and primary prevention.

Fuzhengjiedu formula exerts protective effect against LPS-induced acute lung injury via gut-lung axis

BackgroundAcute lung injury (ALI) is distinguished by rapid and severe respiratory distress and prolonged hypoxemia. A traditional Chinese medicine (TCM), known as the Fuzhengjiedu formula (FZJDF), has been shown to have anti-inflammatory benefits in both clinical and experimental studies. The precise underlying processes, nevertheless, are yet unclear. PurposeThis study sought to enlighten the protective mechanism of FZJDF in ALI through the standpoint of the gut-lung crosstalk. MethodsThe impact of FZJDF on lipopolysaccharide (LPS)-induced ALI murine model were investigated, and the lung injury score, serum interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) expression were measured to confirm its anti-inflammatory effects. Additionally, gut microbiota analysis and serum and fecal samples metabolomics were performed using metagenomic sequencing and high-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry, respectively. ResultsFZJDF significantly induced histopathological changes caused by LPS-induced ALI as well as downregulated the serum concentration of IL-1β and TNF-α. Furthermore, FZJDF had an effect in gut microbiota disturbances, and linear discriminant effect size analysis identified signal transduction, cell motility, and amino acid metabolism as the potential mechanisms of action in the FZJDF-treated group. Several metabolites in the LPS and FZJDF groups were distinguished by untargeted metabolomic analysis. Correlations were observed between the relative abundance of microbiota and metabolic products. Comprehensive network analysis revealed connections among lung damage, gut microbes, and metabolites. The expression of glycine, serine, glutamate, cysteine, and methionine in the lung and colon tissues was dysregulated in LPS-induced ALI, and FZJDF reversed these trends. ConclusionThis study revealed that FZJDF considerably protected against LPS-induced ALI in mice by regulating amino acid metabolism via the gut-microbiota-lung axis and offered thorough and in-depth knowledge of the multi-system linkages of systemic illnesses.

Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure

BackgroundThere is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity. MethodsThis multicenter case–control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances. ResultsShannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE. ConclusionsGut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.

Association of Bacterial Composition and Diversity in the Cervical Tumor Microbiome with HPV Genotype in a Large, International Patient Cohort

Tumor bacterial composition is strongly associated with response to cancer therapy, and is impacted by environment, including geography. Human papillomavirus (HPV) genotypic diversity composition and load are dynamic during pelvic radiation (RT) and correlate with differential responses to RT in cervical cancer patients. In this multi-institutional, collaborative study, we aimed to explore associations between bacterial composition, HPV serotypes, and geographical distribution in an international patient population. Cervical swabs were collected from 287 patients diagnosed with cervical cancer/ dysplasia in four locations: Houston, USA (TX; N = 94), Ethiopia (ETH; N = 85), Puerto Rico (PR; N = 71), and Botswana (BOT; N = 37). Swabs were collected prior to treatment and were subjected to 16S V4 rRNA gene sequencing and HPV genotyping. We compared HPV types and geography via Chi-squared test. We analyzed bacterial composition, alpha diversity (ANOVA), and beta diversity (principal coordinates analysis [PCoA] with PERMANOVA) for HPV type and geography. We used Linear Discriminant Effect Size (LEfSe) analysis to distinguish taxa associated with HPV types. Overall, the global bacterial composition for patients with cancer or dysplasia did not significantly vary by location. However, the proportion of patients with each HPV type varied by location (p<0.01); HPV16 was most frequent in TX (54%), BOT (70%) and ETH (61%), while HPV18 was most frequent in PR (62%). The proportion of patients with HPV low-risk/negative tumors was highest in ETH (25%) compared to other sites (2% - 14%). Patients with HPV 16 had significantly higher bacterial alpha diversity across locations (all p<0.01). The bacterial composition also differed by HPV type across locations (p = 0.01). On LEfSe, bacterial genera enriched in HPV 16 samples were Bacteroides, Clostridium, and Prevotella. Non-HPV16 tumors were enriched in species of Lactobacillus and Gardnerella and HPV 18 and high-risk type tumors were enriched in Escherichia. In thislarge, international cohort of cervical cancer and dysplasia patients, bacterial composition was more closely associated with cervical HPV genotype than with geography. This finding has implications for the development of biomarkers and interventions aimed at improving chemotherapy and radiation response through manipulation of the microbiome.

Respiratory microbiome profiles are associated with distinct inflammatory phenotype and lung function in children with asthma.

Respiratory microbiome studies have fostered our understanding of various phenotypes and endotypes of heterogeneous asthma. However, the relationship between the respiratory microbiome and clinical phenotypes in children with asthma remains unclear. We aimed to identify microbiome-driven clusters reflecting the clinical features of asthma and their dominant microbiotas in children with asthma. Induced sputum was collected from children with asthma, and microbiome profiles were generated via sequencing of the V3-V4 region of the 16S rRNA gene. Cluster analysis was performed using the partitioning around medoid clustering method. The dominant microbiota in each cluster was determined using the Linear Discriminant Effect Size analysis. Each cluster was analyzed for association among the dominant microbiota, clinical phenotype, and inflammatory cytokine. Eighty-three children diagnosed with asthma were evaluated. Among four clusters reflecting the clinical characteristics of asthma, cluster 1, dominated by Haemophilus and Neisseria, demonstrated lower post-bronchodilator (BD) forced expiratory volume in 1 second (FEV1)/forced vital capacity (FVC) than that in the other clusters and more mixed granulocytic asthma. Neisseria negatively correlated with pre-BD and post-BD FEV1/FVC. Haemophilus and Neisseria positively correlated with programmed death-ligand (PD-L)1. To our knowledge, this study is the first to analyze the relationship between an unbiased microbiome-driven cluster and clinical phenotype in children with asthma. The cluster dominated by Haemophilus and Neisseria showed fixed airflow obstruction and mixed granulocytic asthma, which correlated with PD-L1 levels. Thus, microbiome-driven unbiased clustering can help identify new asthma phenotypes related to endotypes in childhood asthma.

Effects of effective microorganisms on the physiological status, intestinal microbiome, and serum metabolites of Eriocheir sinensis.

The compound known as effective microorganisms (EMs) is widely used in aquaculture to improve water quality, but how they affect the health of Chinese mitten crab (Eriocheir sinensis) is unclear, especially in terms of intestinal microbiota and serum metabolites. In this study, we fed juvenile crabs with an EM-containing diet to explore the effects of EM on the physiological status, intestinal microbiome, and metabolites of E. sinensis. The activities of alanine aminotransferase and alkaline phosphatase were significantly enhanced by EM, indicating that EM supplementation effectively enhanced the antioxidant capacity of E. sinensis. Proteobacteria, Tenericutes, Firmicutes, Bacteroidetes, and Actinobacteria were the main intestinal microbes in both the control and EM groups. Linear discriminant effect size analysis showed that Fusobacteriaceae, Desulfovibrio, and Morganella were biomarkers in the control group, and Exiguobacterium and Rhodobacteraceae were biomarkers in the EM group. Metabolomics analysis revealed that EM supplementation increased cellular energy sources and decreased protein consumption, and oxidative stress. Together, these results indicate that EM can optimize the intestinal microbiome and serum metabolites, thereby benefiting the health of E. sinensis.

Gut microbiota alterations in critically Ill patients with carbapenem-resistant Enterobacteriaceae colonization: A clinical analysis.

Carbapenem-resistant Enterobacteriaceae (CRE) are an emerging concern for global health and are associated with high morbidity and mortality in critically ill patients. Risk factors for CRE acquisition include broad-spectrum antibiotic use and microbiota dysbiosis in critically ill patients. Therefore, we evaluated the alteration of the intestinal microbiota associated with CRE colonization in critically ill patients. Fecal samples of 41 patients who were diagnosed with septic shock or respiratory failure were collected after their admission to the intensive care unit (ICU). The gut microbiota profile determined using 16S rRNA gene sequencing and quantitative measurement of fecal short-chain fatty acids were evaluated in CRE-positive (n = 9) and CRE negative (n = 32) patients. The analysis of bacterial metabolic abundance to identify an association between CRE acquisition and metabolic pathway was performed. CRE carriers showed a significantly increased proportion of the phyla Proteobacteria and decreased numbers of the phyla Bacteroidetes as compared to the CRE non-carriers. Linear discriminant analysis (LDA) with linear discriminant effect size showed that the genera Erwinia, Citrobacter, Klebsiella, Cronobacter, Kluyvera, Dysgomonas, Pantoea, and Alistipes had an upper 2 LDA score in CRE carriers. The alpha-diversity indices were significantly decreased in CRE carriers, and beta-diversity analysis demonstrated that the two groups were clustered significantly apart. Among short-chain fatty acids, the levels of isobutyric acid and valeric acid were significantly decreased in CRE carriers. Furthermore, the PICRUSt-predicted metabolic pathways revealed significant differences in five features, including ATP-binding cassette transporters, phosphotransferase systems, sphingolipid metabolism, other glycan degradation, and microbial metabolism, in diverse environments between the two groups. Critically ill patients with CRE have a distinctive gut microbiota composition and community structure, altered short-chain fatty acid production and changes in the metabolic pathways. Further studies are needed to determine whether amino acids supplementation improves microbiota dysbiosis in patients with CRE.

Influence of Organic Amendments Based on Garden Waste for Microbial Community Growth in Coastal Saline Soil

Garden waste compost (GWC) has been applied as an amendment to improve the desalination efficiency, nutrient availability and diversity of the microbial community in coastal saline soil. Understanding the response of the microbial community to garden waste compost application is of great significance in coastal ecological restoration. Four treatments were established: CK, nonamended control; T1, application of 68 kg·m−3 garden waste compost; T2, application of 15 kg·m−3 bentonite; and T3, a mixture of garden waste compost and bentonite. In addition, soil physicochemical properties, soil enzymes, microbial biomass carbon and the soil microbial community were measured. The results show that T3 had a more significant effect on increasing soil enzymes, as well as microbial biomass carbon and nitrogen, urease, sucrase and dehydrogenase activities. Based on the relative abundance, microbial diversity and linear discriminant effect size (LEfSe) analyses, the amendments can be seen to have increased the microbial abundance and alpha diversity of the bacterial structure and also altered the microbial community structure. RDA and Pearson correlation analysis at the phylum level indicated that available nitrogen, total porosity, hydraulic conductivity, bulk density and EC were the primary determinants of microbial communities associated with this amendment. In conclusion, the application of garden waste compost enables more microorganisms to participate in the soil material cycle, indicating that garden waste composting is beneficial to the restoration of coastal soils.

Changes in Phyllosphere Microbial Communities of Pinus tabuliformis after Infestation by Bursaphelenchus xylophilus

Phyllosphere microbial communities have an important role in plant growth and resistance to pathogen infection and are partially influenced by leaf characteristics. Pinewood nematode, Bursaphelenchus xylophilus, is one of the greatest threats to pine trees and is spreading all over the world. However, studies on the resistance of plant–microbe interactions to pathogens during the nematode’s pathogenesis and the relationships of leaf chemical characteristics caused by pinewood nematode and phyllosphere microbial communities are limited. In this study, different stages of Pinus tabuliformis that were healthy or infected with B. xylophilus-associated leaf characteristics and phyllosphere bacterial and fungal communities were compared. These results demonstrated that soluble sugar and starch contents decreased based on the extent of infection. Phyllosphere microbial community changes potentially caused by B. xylophilus infection of P. tabuliformis and the fungal community compositions of healthy P. tabuliformis trees (Ya) were clearly different from diseased P. tabuliformis trees at an early stage of B. xylophilus infection (Yb) and P. tabuliformis trees in the last stage of B. xylophilus infection (Yc), particularly along the first coordinate axis. According to a linear discriminant effect size (LEfSe) analysis, the biomarker species in the phyllosphere of Yb were Acidobacteria, Deinococcus-Thermus, and Patescibacteria, while those in the phyllosphere of Ya were Proteobacteria, Aureobasidium, Dictyosporium, Alternariaster, Knufia, Microstroma, and Naganishia. Particularly at the end of PWD (pine wilt disease) infection, the majority of microbial taxa tended to co-exclude rather than co-occur with PWD infection. The result of a canonical correlation analysis (CCA) showed that the chemical properties of leaves, such as carbon and nitrogen, have significant impacts on phyllosphere microbial communities. These results expanded the possible connections between the phyllosphere communities and plant health.

Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea.

An imbalanced gut microbiome has been linked to a higher risk of many bone-related diseases. The objective of this study was to discover biomarkers of osteoporosis (OP). So, we collected 76 stool samples (60 human controls and 16 OP patients), extracted DNA, and performed 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. Among the taxa with an average taxonomic composition greater than 1%, only the Lachnospira genus showed a significant difference between the two groups. The Linear Discriminant Effect Size analysis and qPCR experiments indicated the Lachnospira genus as a potential biomarker of OP. Moreover, a total of 11 metabolic pathways varied between the two groups. Our study concludes that the genus Lachnospira is potentially crucial for diagnosing and treating osteoporosis. The findings of this study might help researchers better understand OP from a microbiome perspective. This research might develop more effective diagnostic and treatment methods for OP in the future.

Microbiome of Acute Otitis Externa

Ear canal skin is directly attached to bone or cartilage, and is also connected to the eardrum. Acute otitis externa is cellulitis of the ear canal skin and subdermal tissue associated with acute inflammation and variable edema. We characterized the microbiome of the normal ear canal and ear canal with otitis externa. In total, 28 samples (14 each from the ear canal skin of patients with acute otitis externa and normal healthy controls) were collected using swabs. DNA extraction and bacterial microbiome analysis via 16S rRNA gene sequencing were performed. The diversity index (mean amplicon sequence variants and Shannon index) were lower in the otitis externa than control group. According to linear discriminant effect size (LEfSe) analysis, a number of taxa differed significantly between the groups. Pseudomonas at the genus level and Staphylococcus warneri at the species level were identified in the otitis externa group. Our results show the importance of the microbiome in the pathogenesis of otitis externa and provide a basis for treating acute otitis externa by targeting the microbiome.

The structure and assembly of rhizobacterial communities are influenced by poplar genotype.

The interaction between plants and microbes dominates plant growth and fitness in specific environments. The study of the relationship between plant genotypes and rhizobacterial community structure would provide a deep insight into the recruitment strategies of plants toward soil bacteria. In this study, three genotypes of 18-year-old mature poplar (H1, H2, and H3) derived from four different parents were selected from a germplasm nursery of Populus deltoides. Rhizosphere soil carbon, nitrogen, and phosphorus properties as well as the 16S rDNA sequences of rhizobacterial communities were analyzed to determine the relationship between poplar genotypes and rhizobacterial communities assembly. The results showed there were significant differences in the diversity (Chao1, ACE index, and Shannon index) of rhizobacterial communities between H1 and H2, as well as between H2 and H3, but no difference between H1 and H3. Principal component analysis also revealed a similar structure of rhizobacterial communities between H1 and H3, whereas the rhizobacterial communities of H2 demonstrated significant differences from H1 and H3. Linear discriminant effect size analysis indicated that there were 11 and 14 different biomarkers in the H1 and H3 genotype, respectively, but 42 in the H2 genotype. Co-occurrence network analysis indicated that the rhizobacterial communities of H2 had a distinct network structure compared to those of the other two genotypes, whereas H1 and H3 had a similar pattern of co-occurrence network. Threshold indicator taxa analysis revealed that 63 genera responded significantly to NO3 --N content and 58 genera to NH4 +-N/NO3 --N ratio. Moreover, the stochastic assembly process was found to be decreased with increasing NO3 --N content and fluctuated with increasing NH4 +-N/NO3 --N ratio. All results indicated that the structure of poplar rhizobacterial communities were influenced by host genotypes, and available nitrogen might play a dominant role in the assembly of rhizobacterial communities. This study would promote the future selection and utilization of rhizobacteria in poplar breeding.

Characterization of the Tumor-Associated Microbiome Landscapes of HPV-Related Anogenital Cancers

<h3>Purpose/Objective(s)</h3> There is an increasing interest in the composition of tumor-associated microbiomes and their effect on treatment response and patient outcomes. This study aims to explore the differences between the tumor-associated microbiome landscapes of patients diagnosed with HPV-related anogenital cancers. We have previously shown that <i>Lactobacillus iners</i> is associated with poor treatment response among cervical cancer patients, so we studied the presence of <i>L. iners</i> among other anogenital cancers. <h3>Materials/Methods</h3> Tumor swabs were collected from patients diagnosed with cervical cancer (n=85), anal cancer (n=20), vaginal cancer (n=7), and vulvar cancer (n=3) receiving chemoradiation therapy (CRT) from 2 institutions. Samples were collected and analyzed at baseline, week 1, 3, and 5 during CRT and at 3 months post-CRT using 16Sv4 rRNA gene sequencing. Multivariate community-level differences between the tumor microbiomes was conducted using principal coordinates analysis (PCoA) plots and pairwise PERMANOVA. Linear Discriminant Effect Size (LEfSe) analysis was used to identify specific taxa abundant among the different tumor types at baseline and end of treatment. <h3>Results</h3> PERMANOVA revealed significant compositional differences between the cancer types (p= 0.001). There were significant compositional differences between all cancer types (q<0.01 for all), except between vaginal and vulvar cancers (q= 0.12). LEfSe revealed that the microbiome of each cancer was dominated by different bacteria. <i>L. iners</i> was enriched in cervical samples, Clostridia and Bacteroidaceae were enriched in anal samples, Proteobacteria was enriched in vaginal samples, and Peptostreptococcales-Tissierellales and Staphylococcales were enriched in vulvar samples at baseline. Moreover, by the end of treatment, Bifidobacteriales were enriched in cervical samples, while Proteobacteria, Corynebacteriales, and Clostridia were enriched in anal samples, and Bacteroidota was enriched in vulvar samples. Of interest, L. iners was present in two out of three non-responders with anal cancer, and one out of two non-responders with vaginal cancer. However, the proportions of Liners in these patients were less than those in patients with cervical cancer. <h3>Conclusion</h3> Our results show that the tumor microbiomes of HPV-related anogenital cancers differ significantly from each other and have distinct reactions to CRT. These findings could lay the groundwork for interventions tailored to the tumor-specific microbiome to enhance the effectiveness of CRT.

Dynamics of gut microflora across the life cycle of Spodoptera frugiperda and its effects on the feeding and growth of larvae.

Spodoptera frugiperda is an important invasive agricultural pest that causes huge economic losses worldwide. Gut microorganisms play a vital role in host feeding, digestion, nutrition, immunity, growth and insecticide resistance. Illumina high-throughput sequencing was used to study the gut microbial community dynamics across the life cycle (egg, 1st to 6th instar larvae, pupae, and male and female adults) of S.frugiperda fed on maize leaves. Furthermore, the gut microbial community and food intake of the 5th instar S.frugiperda larvae were studied after feeding them antibiotics. Enterobacteriaceae and Enterococcaceae dominated the gut during growth and feeding of the larvae. The relative abundance of Enterobacteriaceae was higher in the 4th and 6th instar larvae. With the increase in larval feeding, the relative abundance of Enterococcaceae gradually increased. In addition, principal coordinate analysis and linear discriminant effect size analysis confirmed differences in the structure of gut microbiota at different developmental stages. After antibiotic treatment, the relative abundance of Firmicutes, Proteobacteria and Fusobacteriota decreased. The relative abundance of Enterococcus and Klebsiella decreased significantly. Antibiotic treatment inhibited the gut flora of S.frugiperda, which decreased larval food intake and body weight gain, and prolonged the larval stage. The composition of the gut bacterial community plays an important role in the growth, development, and feeding of S.frugiperda. The results have a certain theoretical value for the development of bio-pesticides targeting intestinal flora. © 2022 Society of Chemical Industry.