Linear Discriminant Analysis Effect Size Research Articles

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain.

The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

The Effect of Artificial Substrate and Carbon Source Addition on Bacterial Diversity and Community Composition in Water in a Pond Polyculture System

The use of artificial substrates and biofloc technology can favor fish culture and improve water quality. The aim of this study was to evaluate whether artificial substrates and carbon source additions modify the microbial activity of water bodies. The diversity and structure of microflora in the water after adding artificial substrates and carbon sources to the ponds were analyzed using high-throughput sequencing based on the V3-V4 region of 16S rRNA genes. The results showed that there was no difference in the richness and diversity of intestinal microflora between the control and experimental groups. Principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS) showed that artificial substrate and carbon source addition changed the structure of the microflora. The results of a linear discriminant analysis (LDA) effect size (LefSe) indicated 11 biomarkers in the EGˍst group. Spearman correlation heatmap analysis showed that environmental factors affected the bacterial communities, and the results of a redundancy analysis indicated that chemical oxygen demand was a critical factor in controlling the bacterial communities in the water. These results provide an understanding of the effect of artificial substrate and carbon source addition on bacterial diversity and community composition in water.

Predicting the role of the human gut microbiome in type 1 diabetes using machine-learning methods.

Gut microbes is a crucial factor in the pathogenesis of type 1 diabetes (T1D). However, it is still unclear which gut microbiota are the key factors affecting T1D and their influence on the development and progression of the disease. To fill these knowledge gaps, we constructed a model to find biomarker from gut microbiota in patients with T1D. We first identified microbial markers using Linear discriminant analysis Effect Size (LEfSe) and random forest (RF) methods. Furthermore, by constructing co-occurrence networks for gut microbes in T1D, we aimed to reveal all gut microbial interactions as well as major beneficial and pathogenic bacteria in healthy populations and type 1 diabetic patients. Finally, PICRUST2 was used to predict Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways and KO gene levels of microbial markers to investigate the biological role. Our study revealed that 21 identified microbial genera are important biomarker for T1D. Their AUC values are 0.962 and 0.745 on discovery set and validation set. Functional analysis showed that 10 microbial genera were significantly positively associated with D-arginine and D-ornithine metabolism, spliceosome in transcription, steroid hormone biosynthesis and glycosaminoglycan degradation. These genera were significantly negatively correlated with steroid biosynthesis, cyanoamino acid metabolism and drug metabolism. The other 11 genera displayed an inverse correlation. In summary, our research identified a comprehensive set of T1D gut biomarkers with universal applicability and have revealed the biological consequences of alterations in gut microbiota and their interplay. These findings offer significant prospects for individualized management and treatment of T1D.

Characteristics of bacterial community in eyelashes of patients with Demodex blepharitis

BackgroundDemodex blepharitis (DB) is a common disease of the ocular surface. The characteristics of the bacterial community in eyelash roots after Demodex infestation are still unknown. Knowledge of the characteristics of the bacterial community of eyelash follicles in patients with DB can provide valuable insights for guiding the diagnosis and treatment of DB.MethodsTwenty-five patients with DB (DB group) and 21 non-DB volunteers (control group) were enrolled in the study. Eyelashes from the upper eyelid of the right eye were sampled, and 16S ribosomal DNA (rDNA) sequencing was performed to determine the V3-V4 regions of the microbial 16S rDNA gene within 1 month of infestation. The sequencing data of the two groups were analyzed and compared. The effect of the bacterium Burkholderia on the survival of Demodex mites was evaluated using Demodex obtained from 12 patients with DB other that the patients in the DB group.ResultsA total of 31 phyla and 862 genera were identified in the DB and control groups. The five most abundant phyla in the two groups were Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria. The abundance of Actinomycetes was significantly higher in the DB group than in the control group. At the genus level, the five most abundant genera in the two groups were Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, Rolstonia and Acinetobacter; Clostridium sensu stricto 1 was abundant in the control group and Corynebacterium_1 was abundant in the DB group. Compared with the control group, the abundance of Burkholderia-Caballeronia-Paraburkholderia was 2.36-fold lower in the DB group. Linear discriminant analysis Effect Size (LEfSe) analysis revealed Burkholderia-Caballeronia-Paraburkholderia, SC_I_84_unclassified, Nonmyxobacteria and Succinvibrio to be the major biomarkers in the control group and Catenibacterium and Lachnospiraceae NK4A136 group to be the major biomarkers in the DB group. To explore the performance of these optimal marker models, receiver operational characteristic curve analysis was performed, and the average area under the curve value of Burkholderia-Caballeronia-Paraburkholderia was 0.7448. Burkholderia cepacia isolated from normal human eyelashes was fermented, and the Demodex mites isolated from patient eyelashes were cultured together with its fermented supernatant. The results showed that the fermentation supernatant could significantly reduce the survival time of the Demodex mites, suggesting the potential therapeutic value of this bacterium against Demodex.ConclusionsThe composition of the bacterial community in the eyelashes of DB patients differed from that in eyelashes of healthy volunteers, revealing a decrease in bacterial diversity in infested eyelashes. This decrease may be related to the occurrence and development of DB. The supernatant of Burkholderia cepacia culture medium was found to inhibit the growth of Demodex in eyelash hair follicles, providing a new insight with potential applications for the clinical treatment of Demodex infestation.Graphical

Gut microbiota was highly related to the immune status in chronic obstructive pulmonary disease patients.

This study aimed to explore the profile of gut microbiota and immunological state in COPD patients. 80 fecal and blood samples were collected from 40 COPD patients and 40 healthy controls (HC) and analyzed with 16s-rRNA gene sequencing and immunofactor omics analysis to investigate the profile of gut microbiota and immunologic factors (IFs). The linear discriminant analysis (LDA) effect size (LefSe) was used to determine the biomarker's taxa. The random forest and LASSO regression analysis were executed to screen IFs and develop an IFscore model. The correlation between gut microbiota and IFs, along with the IFscore and the diversity of gut microbiota, was evaluated with the Spearman analysis. The α and β diversity showed that the composition and distribution of gut microbiota in the COPD group differed from that of the HC group. 7 differential taxa at the phylum level and 17 differential taxa at the genus level were found. LefSe analysis screened out 5 biomarker's taxa. 32 differential IFs (up-regulated 27 IFs and down-regulated 5 IFs) were identified between two groups, and 5 IFs (CCL3, CXCL9, CCL7, IL2, IL4) were used to construct an IFscore model. The Spearman analysis revealed that 29 IFs were highly related to 5 biomarker's taxa and enriched in 16 pathways. Furthermore, the relationship between the IFscore and gut microbiota diversity was very close. The gut microbiota and IFs profile in COPD patients differed from that in healthy individuals. Gut microbiota was highly related to the immune status in COPD patients.

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.

Research Note: The effect of photoperiod on the NLRP3 inflammasome and gut microbiota in broiler chickens

The present study aimed to investigate the effect of photoperiod on the intestinal inflammation and gut microbiota. A total of 96 broiler chickens were divided into 2 groups and fed separately under 2 different photoperiods (12L:12D group and 23L:1D group) for 21 d. The results showed that the photoperiod of 23L:1D damaged duodenal tissue structure (intestinal villus erosion, mucosal epithelial cell detachment, and inflammatory cell infiltration), significantly increased the concentration of inflammatory cytokines (IL-1β, IL-18, IL-6, and TNF-α) and significantly increased the mRNA expression levels and protein expression levels of NOD-, LRR-, pyrin domain-containing protein 3 (NLRP3) and caspase1 (P <0.05) compared with 12L:12D, which indicating that extended photoperiod induced intestinal injury and activated NLRP3 inflammasome. 16S rRNA sequencing analysis revealed that Bacteroides was significantly decreased, Ruminococcus_torques_group, norank_f_Desulfovibrionaceae, GCA-900066575, Defluviitaleaceae_UCG-011, Lachnospiraceae_FCS020_group, norank_f_UCG-010 and norank_f_norank_o_Clostridia_vadinBB60_group and were significantly increased in the 23L:1D group, compared with the 12L:12D group (P < 0.05). The correlation analysis between differential microbial communities and intestinal inflammation showed that the relative abundance of Bacteroides was negatively correlated with the mRNA expression level of NLRP3 (P < 0.05) and the relative abundance of Ruminococcus_torques_group was positively correlated with the mRNA expression level of NLRP3 (P < 0.05). linear discriminant analysis (LDA) effect size (LEfSe) results (LDA > 4) showed that the relative abundance of Bacteroides was dramatically higher (P < 0.05) in the 12L:12D group, whereas the relative abundance of Ruminococcus_torques_group was noticeably higher (P < 0.05) in the 23L:1D group. By the comprehensive analysis of the gut microbiota, the interaction of gut microbiota (Bacteroides and Ruminococcus_torques_group) and NLRP3 inflammasome may contribute to the intestinal injury under the condition of extended photoperiod.

Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study

ObjectivesAlcohol consumption is not uncommon among people with HIV (PWH) and may exacerbate HIV-induced intestinal damage, and further lead to dysbiosis and increased intestinal permeability. This study aimed to determine the changes in the faecal microbiota and its association with alcohol consumption in HIV-infected patients. MethodsA cross-sectional survey was conducted between November 2021 and May 2022, and 93 participants were recruited. To investigate the alterations of alcohol misuse on fecal microbiology in HIV-infected individuals, we performed 16s rDNA gene sequencing on fecal samples from the low to moderate drinking (n=21) and non-drinking (n=72) groups. ResultsComparison between groups using alpha and beta diversity showed that the diversity of stool microbiota in the low to moderate drinkinge group did not differ from that of the non-drinking group (all P>0.05). The Linear discriminant Analysis effect size (LEfSe) algorithm was to determine the bacterial taxa associated with alcohol consumption, and the results showed altered fecal bacterial composition in HIV-infected patients who consumed alcohol, with Coprobacillus, Pseudobutyrivibrio and Peptostreptococcaceae enriched, and Pasteurellaceae and Xanthomonadaceae were depleted. In addition, by using the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional microbiome features were also found to be altered in the low to moderate drinking group, showing a reduction in metabolic pathways (P=0.036) and cardiovascular disease pathway (P=0.006). ConclusionLow to moderate drinking will change the composition, metabolism and cardiovascular disease pathway of the gut microbiota of HIV-infected patients.

Fungal communities associated with early immature tubers of wild Gastrodia elata.

Full myco-heterotrophic orchid Gastrodia elata Bl. is widely distributed in Northeast Asia, and previous research has not fully investigated the symbiotic fungal community of its early immature tubers. This study utilized Illumina sequencing to compare symbiotic fungal communities in natural G. elata immature tubers and their habitats. LEfSe (Linear Discriminant Analysis Effect Size) was used to screen for Biomarkers that could explain variations among different fungal communities, and correlation analyses were performed among Biomarkers and other common orchid mycorrhizal fungi. Our results illustrate that the symbiotic fungal communities of immature G. elata tubers cannot be simply interpreted as subsets of the environmental fungal communities because some key members cannot be traced back to the environment. The early growth of G. elata was related to a small group of fungi, such as Sebacina, Thelephora, and Inocybe, which were also common mycorrhizal fungi from other orchids. In addition, Mycena, Auricularia, and Cryptococcus were unique fungal partners of G. elata, and many new species have yet to be discovered. Possible symbiotic Mycena should be M. plumipes and its sibling species in this case. Our results provide insight into the symbiotic partner switch and trophic pattern change during the development and maturation of G. elata.

Differential Abundances of Bdellovibrio and Rheinheimera in the Oral Microbiota of Neonates With and Without Clinical Sepsis.

Neonatal sepsis is associated with high rates of morbidity and mortality, long hospital stays and high cost of care, thereby inflicting a burden on health care systems. Oral care with breast milk has been shown to modify the intestinal tract microbiota and immune system. Herein, we attempted to identify probiotics that may be beneficial to prevent or treat neonatal sepsis. This was a secondary analysis comparing the microbiota during oropharyngeal care in very-low-birth-weight infants with and without clinical sepsis. Oral samples were collected before oral feeding was initiated. The primary outcome was oral microbiota composition including diversity, relative abundance and linear discriminant analysis effect size. Sixty-three neonates, including 39 and 24 with and without clinical sepsis, respectively, were enrolled. The medians gestational age and birth weight were 29 (27-30) weeks and 1010 (808-1263) g. Neonates with clinical sepsis had lower gestational age, birth weight (both P < 0.001) and lower rate of oral care with breast milk (P = 0.03), but higher doses and days of antibiotic exposure (both P < 0.001) compared to neonates without clinical sepsis. No differences in alpha and beta diversities were found between groups and Streptococcus agalactiae was the most common bacteria in both groups. Linear discriminant analysis effect size analysis revealed that neonates without clinical sepsis had significantly higher abundances of order Bdellovibrionales, family Bdellovibrionaceae, genus Bdellovibrio and genus Rheinheimera. Neonates without clinical sepsis had a significantly greater abundance of the Bdellovibrio and Rheinheimera genera.

Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach

Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3–1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.

Comparison of mucosal microbiomes from biliary tract among patients with extrahepatic cholangiocarcinoma, patients with chronic cholecystitis, and healthy controls.

550 Background: Cholangiocarcinoma (CCA) is a malignancy associated with a poor prognosis. Gut microbiome dysbiosis is considered to be related with multiple disease, including and cancer. However, relationship between mucosal microbiome dysbiosis and CCA remains unclear. In this study, we evaluated mucosal microbiome of patients with extrahepatic-CCA (EH-CCA) and compared it with patients with chronic cholecystitis (CC) and living liver donors who served as healthy control (HC), to understand the role of microbiome in development EH-CCA. Methods: A total of 18 patients with EH-CCA, 21 patients with CC, and 17 HC were included. During operation, swab sample were obtained from cancer tissue of patient with EH-CCA and from gallbladder in other participants, respectively. The bacterial 16S rRNA gene (V3/V4 region) was amplified using PCR and sequenced on the Illumina MiSeq platform. The QIIME 2 pipelines were used to analyze the raw data. Results: The median age were 71, 53, and 29 years for patients with EH-CCA, patients with CC, and HC, respectively. The mean number of operational taxonomic unit were significantly higher in the CCA (13,037 [SD 9,676]) compared to HC (5,045 [12,679]; p&lt;0.001). Among the sample from HC, the most abundant taxa at phylum level was Firmicutes (74.47%), followed by Bacteroidota (14.8%), and Proteobacteria accounted for only 2%. In the CC group, Firmicutes is most abundant (63.15%) phylum, followed by Proteobacteria (22.09%). In contrast, among the samples from CCA, Proteobacteria were the most common phylum (50.43%). Pairwise comparison of α-diversity measured by Chao1 index showed that richness was higher in samples from CC compared to other groups (vs HC, p=0.02; vs CCA, p&lt;0.001). In terms of α-diversity measured by Shannon index, samples from cancer have lower diversity compared to healthy controls ( p&lt;0.001), however, no significant differences were found between samples from cancer and CC ( p=0.1). The Principal Coordinate Analysis plot based on Bray-Curtis distance showed that all three groups formed significantly separate clusters (p=0.001). The linear discriminant analysis effect size showed that the most abundant taxa from samples from CCA were Enterobacter, Klebsiella, and Fusobacterium. In the samples from HC, Limosilactobacillus, Lachnospiraceae_NK4A136_group, and Faecalibacterium were most significant, while Lactobacillus and Pseudomonas were most abundant among the CC group. Conclusions: This study compared the mucosal microbiome from biliary tract among patients with CCA, patients with CC, and HC. All three groups showed significantly different microbiome profiles. In CCA sample, the proportion of Proteobacteria is high, and diversity were low, suggesting mucosal microbial dysbiosis. Further studies are needed to investigate the clinical implications of microbial dysbiosis in CCA.

The succession of rhizosphere microbial community in the continuous cropping soil of tobacco

Introduction: Flue-cured tobacco is an important economic crop that is not tolerant of continuous cropping and can be influenced by planting soil conditions including rhizosphere microbial communities and soil physicochemical properties. The relationship between rhizosphere microbial communities and soil physicochemical properties under continuous cropping conditions is unclear.Methods: This study investigated the succession of rhizosphere microbial community in continuous tobacco cropping soil for 1, 3, 5, 8, 10, 15, and 30 years. The physicochemical properties of the soil were measured, high-throughput sequencing was performed on the rhizosphere microbial community, and correlation analysis was conducted.Results: The results suggested that continuous cropping could significantly enrich soil available nitrogen, available phosphorus, available potassium, and organic matter. Meanwhile, the alpha diversity of the bacterial community was significantly reduced with continuous cropping, indicating significant changes in the structure of bacterial and fungal communities. Based on linear discriminant analysis effect size (LEfSe), 173 bacterial and 75 fungal genera were identified with significant differences. The bacterial genera, Sphingomonas, Streptomyces, and Microvirga, were significantly positively correlated with continuous cropping years. The fungal genera, Tausonia, Solicocozyma, Pseudomycohila, and Fusarium, also showed significant positive correlation with continuous cropping years. Meanwhile, the fungal genera, Olpidium, Cephaliophora, and Cercophora, presented an opposite correlation. However, there are differences in the correlation between these bacterial and fungal genera related to continuous cropping years and other different soil physicochemical properties.Discussion: In summary, this work could provide a reference for soil management and scientific fertilization of tobacco under continuous cropping conditions.

Sex-specific differences in intestinal microbiota associated with cardiovascular diseases

BackgroundCardiovascular diseases (CVD), including coronary heart disease (CHD), display a higher prevalence in men than women. This study aims to evaluate the variations in the intestinal microbiota between men and women afflicted with CHD and delineate these against a non-CVD control group for each sex.MethodsOur research was conducted in the framework of the CORDIOPREV study, a clinical trial which involved 837 men and 165 women with CHD. We contrasted our findings with a reference group of 375 individuals (270 men, 105 women) without CVD. The intestinal microbiota was examined through 16S metagenomics on the Illumina MiSeq platform and the data processed with Quiime2 software.ResultsOur results showed a sex-specific variation (beta diversity) in the intestinal microbiota, while alpha-biodiversity remained consistent across both sexes. Linear discriminant analysis effect size (LEfSe) analysis revealed sex-centric alterations in the intestinal microbiota linked to CVD. Moreover, using random forest (RF) methodology, we identified seven bacterial taxa—g_UBA1819 (Ruminococcaceae), g_Bilophila, g_Subdoligranulum, g_Phascolarctobacterium, f_Barnesiellaceae, g_Ruminococcus, and an unknown genus from the Ruminococcaceae family (Ruminococcaceae incertae sedis)—as key discriminators between men and women diagnosed with CHD. The same taxa also emerged as critical discriminators between CHD-afflicted and non-CVD individuals, when analyzed separately by sex.ConclusionOur findings suggest a sex-specific dysbiosis in the intestinal microbiota linked to CHD, potentially contributing to the sex disparity observed in CVD incidence.Trial registration Clinical Trials.gov.Identifier NCT00924937.Graphical

Fecal Microbiota and Feeding Habitats of Nomadic Indigenous Animals (Deer, Yak, Sheep and Camel) in Baikal Siberia (Russia)

In the vast expanse of Baikal Siberia, indigenous nomadic animal groups have been conserved, grazing on pastures throughout the year. It is believed that the fecal microbiota of these diverse nomadic animal species is unique to each species and closely tied to their feeding environments. We conducted a pioneering comparative analysis of the taxonomic structure and the diversity of fecal microbiota in indigenous nomadic animals inhabiting Baikal Siberia. Our study encompassed 20 deer, 23 yaks, 24 camels, and 29 sheep, using high-throughput 16S rRNA gene profiling. In the fecal microbiota of these animals, we observed a predominant presence of the phyla Bacillota, Bacteroidota, and Verrucomicrobiota, collectively comprising over 88% of the microbial communities. Moreover, these proportions exhibited variations according to the host species. The unculturable Bacillota UCG-005 and UCG-010 are the key groups for all animals. However, at the genus level, distinctive compositions of fecal microbiota were discernible within each animal group. We identified a total of 37 dominant genera across the fecal samples from these four animal species. Principal component analysis (PCA) and cluster analysis demonstrated that the fecal microbiota composition clustered among individuals of the same animal species. Linear discriminant analysis effect size (LEfSe) indicated that camels exhibited higher abundances of the family Akkermansiaceae and the uncultured clostridial lineage UCG-010, while deer featured Lachnospiraceae; sheep had Ruminococcaceae; and yaks displayed Monoglobaceae, Bacteroidaceae, and methanogenic archaea from the family Methanobacteriaceae as distinctive marker taxa. Our studies showed that the studied nomadic animals feed mainly on plants belonging to the families Poaceae, Cyperaceae, Asteraceae, and Rosaceae. Our research indicated that the identity of the host species and, to a lesser degree, their diets and habitats, significantly shape the composition of fecal microbiota in these studied nomadic ruminant animals.

Zooming in on the intracellular microbiome composition of bacterivorous Acanthamoeba isolates.

Acanthamoeba, a free-living amoeba in water and soil, is an emerging pathogen causing severe eye infection known as Acanthamoeba keratitis. In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (P < 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (P < 0.017), and Bacteroidota was abundant in Australian water isolates (P < 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (P < 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (P > 0.05). More diverse intracellular bacteria were identified in water isolates as compared with clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens.

Tryptophan metabolites and gut microbiota play an important role in pediatric migraine diagnosis

BackgroundThe pathogenesis of pediatric migraine remains unclear and presents challenges in diagnosis. Recently, growing evidence has indicated that the gut microbiota can exert modulatory functions at the gut-brain axis by directly or indirectly regulating tryptophan metabolism. Consequently, we aimed to elucidate the potential association among gut microbiota, tryptophan metabolism, and pediatric migraine while also identifying diagnostic biomarkers for pediatric migraine.MethodsThe gut microbiota composition of 33 migraine children and 42 healthy children, aged less than ten years, from the GMrepo database, was analyzed using the Shannon index, Simpson index, principal coordinates analysis, and Wilcoxon rank-sum test. Microbial diagnostic biomarkers were identified using linear discriminant analysis effect size, ridge regression, and random forest. Plasma concentrations of tryptophan metabolites investigated by enzyme-linked immunosorbent assay were compared between 51 migraine children and 120 healthy children, aged less than eighteen years, using t tests and analysis of variance. The receiver operating characteristic curve was performed to evaluate the diagnostic value of microbial and metabolite biomarkers in pediatric migraine.ResultsDifferences in the composition of gut microbiota, notably the genera that regulate tryptophan metabolism, were observed in pediatric migraine children. Further investigations revealed a significant decrease in plasma kynurenic acid levels (p < 0.001) among migraine children, along with a significant increase in serotonin (p < 0.05) and quinolinic acid (p < 0.001). Subsequently, we established the normal reference intervals for plasma concentrations of tryptophan metabolites in children. More importantly, the ratio of kynurenic acid to quinolinic acid (AUC: 0.871, sensitivity: 86.3%, specificity: 83.3%) exhibited excellent diagnostic efficacy for pediatric migraine.ConclusionOur study suggests that the gut microbiota may play an important role in the development of pediatric migraine by regulating tryptophan metabolism. We believe that microbial and metabolite biomarkers are sensitive diagnostic tests for pediatric migraine.Trial registrationThe study was registered at ClinicalTrials.gov (NCT05969990).

Organic fertilizer compost alters the microbial composition and network structure in strongly acidic soil

Soil acidification impairs plant growth and agricultural sustainability, whereas organic fertilizers can ameliorate soil quality. Nonetheless, the response of microbial populations to organic fertilization in acidified soil remains elusive. This study selected facility soils that underwent acidification, and native vegetation (Native) soils were used as controls. We investigated the effects of the sole application of inorganic fertilizers, sole application of organic fertilizers, and combined application of organic and inorganic fertilizers on the microbial diversity of rhizosphere soils of tomato (Solanum lycopersicum. L). The effects of applying organic fertilizers on the function of microbial communities and the structure of related networks were analyzed. Results indicated that organic fertilizer enhanced bacterial network complexity, metabolic function, and convergence of the community structure of Native soils. Beneficial biomarkers Gemmatimonadetes, Armatimonadetes, Sphingomonadales, Patescibacteria, Pezizomycetes, and Agaricomycetes were identified by linear discriminant analysis effect size screening. Applying organic fertilizer alters microbial composition, enhancing microbial abundance and network stability in acidified soil. This research reveals the intrinsic mechanism of yield enhancement by organic fertilizers and provides a basis for screening biocontrol strains.

Stool Microbiome Signature Associated with Response to Neoadjuvant Pembrolizumab in Patients with Muscle-invasive Bladder Cancer

Neoadjuvant pembrolizumab has been shown to be a valid treatment for patients affected by muscle-invasive bladder cancer (MIBC), as demonstrated in the PURE-01 clinical trial (NCT02736266). Among the tumor-extrinsic factors influencing immunotherapy efficacy, extensive data highlighted that the microbiome is a central player in immune-mediated anticancer activity. This report aimed to investigate the composition and role of stool microbiome in patients enrolled in the PURE-01 clinical trial. An orthotopic animal model of bladder cancer (MB49-Luc) was used to support some of the findings from human data. An analysis of stool microbiome before pembrolizumab was conducted for 42 patients, of whom 23 showed a pathologic response. The information in the preclinical model of orthotopic bladder cancer treated with anti–PD-1 antibody or control isotype was validated. Linear discriminant analysis effect size and linear models were used to identify the bacterial taxa enriched in either responders or nonresponders. The identified taxa were also tested for their association with event-free survival (EFS). Survival at 31 d after tumor instillation was used as the study endpoint in the preclinical model. Responders and nonresponders emerged to differ in terms of enrichment for 16 bacterial taxa. Of these, the genus Sutterella was enriched in responders, while the species Ruminococcus bromii was enriched in nonresponders. The negative impact of R. bromii on anti–PD-1 antibody activity was also observed in the preclinical model. EFS and survival of the preclinical model showed a negative role of R. bromii. We found different stool bacterial taxa associated with the response or lack of response to neoadjuvant pembrolizumab. Moreover, we provided experimental data about the negative role of R. bromii on immunotherapy response. Further studies are needed to externally validate our findings and provide mechanistic insights about the host-pathogen interactions in MIBC. Patient summaryUsing prepembrolizumab stool samples collected from patients enrolled in the PURE-01 clinical trials, we identified some bacterial taxa that were enriched in patients who either responded or did not respond to immunotherapy. Using an animal model of bladder cancer, we gathered further evidence of the negative impact of the Ruminococcus bromii on immunotherapy efficacy. Further studies are needed to confirm the current findings and test the utility of these bacteria as predictive markers of immunotherapy response.

Analysis of intestinal flora in elderly Uygur patients with sarcopenia.

This study was designed to analyze the structural characteristics of the intestinal flora of elderly Uygur patients with sarcopenia, thereby providing new ideas for clinical treatment. Firstly, fecal samples were collected from 40 elderly Uygur patients with sarcopenia (Sarcopenia group) and 40 healthy people (Control group). Next, significant differences in the intestinal flora between the two groups were analyzed based on 16S rDNA high-throughput sequencing. The linear discriminant analysis effect size (LEfSe) was used to estimate the magnitude of the effect of each component (species) abundance on the differential effect. Additionally, an analysis was also performed on the relationship between the intestinal flora and the cytokines in the peripheral blood of patients with sarcopenia. The results of β diversity showed that there were differences in the structure of the intestinal flora between the two groups. Besides, the phylum level of intestinal flora between the two groups was not significantly different. However, the difference was significant in the intestinal flora at the order, family, and genus levels between the two groups. Among them, Lachnoclostridium, Photobacterium, Anaerobic Bacillus, Hydrogenophilus, and Eubacterium were enriched in the Sarcopenia group; Prevotella 9, Firmicutes FCS020 group, Streptobacillus, Aggregatibacter, Corynebacterium, Clostridium Difficile, and Haloanaerobium were enriched in the Control group. The LEfSe outcomes further showed that Lachnoclostridium was highly enriched in the Sarcopenia group; Prevotella 9 and Firmicutes FCS020 group were significantly enriched in the Control group. Furthermore, the relative abundance of Lachnoclostridium and Streptobacillus were significantly different in patients with high and low IL-6 levels. In conclusion, Lachnoclostridium is significantly enriched in the intestines of elderly Uygur patients with sarcopenia; the increase in Lachnoclostridium abundance and the decrease in Streptobacillus abundance are associated with high levels of IL-6. Therefore, abnormal intestinal flora is related to inflammatory reflexes in patients with sarcopenia.