Linear Discriminant Analysis Effect Size Research Articles

Characteristics and health impacts of bioaerosols in animal barns: A comprehensive study

Bioaerosols produced during animal production have potential adverse effects on the health of workers and animals. Our objective was to investigate characteristics, antibiotic-resistance genes (ARGs), and health risks of bioaerosols in various animal barns. Poultry and swine barns had high concentrations of airborne bacteria (11156 and 10917 CFU/m3, respectively). Acinetobacter, Clostridium sensu stricto, Corynebacterium, Pseudomonas, Psychrobacter, Streptococcus, and Staphylococcus were dominant pathogenic bacteria in animal barns, with Firmicutes being the most abundant bacterial phylum. Based on linear discriminant analysis effect size (LEfSe), there were more discriminative biomarkers in cattle barns than in poultry or swine barns, although the latter had the highest abundance of bacterial pathogens and high abundances of ARGs (including tetM, tetO, tetQ, tetW sul1, sul2, ermA, ermB) and intI1). Based on network analyses, there were higher co-occurrence patterns between bacteria and ARGs in bioaerosol from swine barns. Furthermore, in these barns, relative abundance of bacteria in bioaerosol samples was greatly affected by environmental factors, mainly temperature, relative humidity, and concentrations of CO2, NH3, and PM2.5. This study provided novel data regarding airborne bio-contaminants in animal enclosures and an impetus to improve management to reduce potential health impacts on humans and animals.

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study.

Periodontitis is a potential risk factor for preterm birth (PTB) in women; however, the causal relationship or the exact mechanism remain unknown. This study aimed to compare the oral microbiome features of mothers with full-term birth (FTB) with those who had preterm delivery. This study prospectively enrolled 60 women (30 mothers with PTB and 30 mothers with FTB), and subgingival plaque samples were collected and analysed by metagenomic 16S rDNA sequencing. Clinical measurements, including periodontal probing depth, clinical attachment level, modified gingival index (mGI) and plaque index, were performed to determine the periodontal state of the participants. Medical and obstetric data were collected as well. Among the periodontal measurements, mGI score, reflecting the level of gingival inflammation, exhibited a statistically significant association with PTB (adjusted odds ratio 2.705, 95% confidence interval 1.074-6.811, p = .035). When subgroup analysis was conducted based on mean mGI scores (mGI ≥ 2, high inflammation [HI] versus mGI < 2, low inflammation [LI]), microbiome analysis revealed clear distinctions in microbial compositions between PTB and FTB mothers in both the HI and LI groups. Especially in the HI group, alpha diversity exhibited a decreasing trend in PTB mothers compared to FTB mothers. Beta diversity also revealed significant differences between the two groups. In Linear Discriminant Analysis Effect Size analysis, certain anaerobic taxa, including the genera Spirochaetes, Treponema and Porphyromonas, were relatively abundant in the FTB/HI group, whereas the PTB/HI group showed a high abundance of the order Actinomycetales. Network analysis showed that the FTB/HI had relatively stronger connectivity in microbial composition than the PTB/HI group. Dysbiosis ratio of plaque microbiome, in terms of periodontitis, was significantly lower in PTB/HI group compared to FTB/HI group. The compositions of maternal subgingival microbiomes differed between PTB and FTB mothers in both the high and low levels of gingival inflammation groups. In the presence of high level of gingival inflammation, dysbiosis in plaque microbiome, in terms of periodontitis, was decreased in PTB mothers compared to FTB mothers.

Oral microbiome sequencing revealed the enrichment of Fusobacterium sp., Porphyromonas sp., Campylobacter sp., and Neisseria sp. on the oral malignant fibroma surface of giant panda

IntroductionMicrobial community composition is closely associated with host disease onset and progression, underscoring the importance of understanding host–microbiota dynamics in various health contexts.MethodsIn this study, we utilized full-length 16S rRNA gene sequencing to conduct species-level identification of the microorganisms in the oral cavity of a giant panda (Ailuropoda melanoleuca) with oral malignant fibroma.ResultsWe observed a significant difference between the microbial community of the tumor side and non-tumor side of the oral cavity of the giant panda, with the latter exhibiting higher microbial diversity. The tumor side was dominated by specific microorganisms, such as Fusobacterium simiae, Porphyromonas sp. feline oral taxon 110, Campylobacter sp. feline oral taxon 100, and Neisseria sp. feline oral taxon 078, that have been reported to be associated with tumorigenic processes and periodontal diseases in other organisms. According to the linear discriminant analysis effect size analysis, more than 9 distinct biomarkers were obtained between the tumor side and non-tumor side samples. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the oral microbiota of the giant panda was significantly associated with genetic information processing and metabolism, particularly cofactor and vitamin, amino acid, and carbohydrate metabolism. Furthermore, a significant bacterial invasion of epithelial cells was predicted in the tumor side.DiscussionThis study provides crucial insights into the association between oral microbiota and oral tumors in giant pandas and offers potential biomarkers that may guide future health assessments and preventive strategies for captive and aging giant pandas.

#395 Gut dysbiosis in ADPKD patients: a controlled pilot study

Abstract Background and Aims Gut dysbiosis has been associated with chronic kidney disease (CKD) and nephrolithiasis and may thus be a factor explaining variability of outcome in autosomal dominant polycystic kidney disease (ADPKD). However, beside a single pilot study the gut microbiome has not been studied in ADPKD. Due to the implications of microbiota in inflammation and crystal formation, we hypothesized that gut dysbiosis could also negatively affect PKD. For this reason, we aimed to characterize the intestinal microbiome in a controlled pilot study of PKD patients and explore the potential impact of dysbiosis on PKD disease progression. Method This study was designed as an observational, cross-sectional controlled pilot study. 25 ADPKD patients were recruited from the AD(H)PKD patient cohort. 12 healthy control subjects were age- and sex matched. Patients with chronic bowel disease were excluded. Serum parameters including eGFR were analyzed around the timepoint of stool collection. The gut microbiome was analyzed by 16S rRNA gene profiling of stool samples. The sequencing data was processed using the DADA2 pipeline and QIIME version 2. Differentially abundant features were identified using linear discriminant analysis (LDA) effect size (LEfSe) analysis. Bacteria-derived serum uremic toxins (total and free Trimethylaminoxid, Indoxylsulfate, p-Cresyl-Sulfate) were measured using liquid chromatography coupled to tandem mass spectrometry (LC- MS/MS). Microbiome data was then correlated with age, kidney function, and markers of PKD disease progression like Mayo classification and early onset of arterial hypertension or urologic complications (&amp;lt;35 years of age). Results Healthy control subjects revealed a significantly higher abundance Actinobacteria (LEfSe LDA score = 3.9, p = 0.025) including probiotic Bifidobacteriaceae (LEfSe LDA score = 3.9, p = 0.021). ADPKD patients displayed a significantly increased abundance of potentially dysbiotic Enterobacteriaceae (LEfSe LDA score = 3.6, p = 0.009). Those findings were independent of kidney function. Most notably, the abundance of Streptococcaceae were significantly overrepresented in PKD patients with Mayo Classes 1D and 1E compared to 1A-1C (p = 0.011). Additionally, early onset of hypertension (&amp;lt; 35 years of age) was associated with an increased abundance of potentially dysbiotic Proteobacteria and a decreased abundance of potentially probiotic Tannerelleaceae. Furthermore, ADPKD patients revealed increased abundance of Peptococcaceae with increasing age and declining kidney function. Finally, serum uremic toxins were significantly increased in ADPKD patients and highly correlated with eGFR. Serum uremic toxins revealed a tendency of positive correlation with the abundance of Peptococcaceae which did not reach statistical significance. Conclusion This controlled pilot study confirms alterations of specific OTUs in PKD patients showing an increase of Enterobacteriaceae and decrease of probiotic Bifidobacteriaceae upon PKD. This suggests a potential shift towards gut dysbiosis. Most notably, the abundance of specific OTUs were observed to be associated with markers of rapid disease progression like Mayo classification 1D and 1E, as well as early onset of arterial hypertension. This suggests for the first time, that gut dysbiosis could affect PKD disease progression. However, it still remains unknown whether gut dysbiosis is caused by ADPKD itself or is a consequence of secondary circumstances such as antibiotic treatment which is common in ADPKD due to frequent urinary tract or cyst infections. Thus, further investigation in larger cohorts is warranted to elucidate the impact of gut microbiota on ADPKD.

Measuring the impact of dietary supplementation with citrus or cucumber extract on chicken gut microbiota using 16s rRNA gene sequencing.

This study investigated the effects of dietary supplements, citrus (CTS) and cucumber (CMB), on the jejunum and cecum microbiota of 14- and 28-days old broiler chickens to evaluate their impact on the gut health and assess their role as alternatives to antibiotic growth promoters (ABGPs). 16SrRNA gene sequencing revealed the overall bacterial microbiota composition was significantly affected by the gut site (p?<?0.001) but not by either of the dietary supplements, CTS and CMB, at both 14 and 28 days of age. However, as a result of Linear discriminant analysis (LDA) effect size (LEfSE), CTS dietary supplements significantly increased the counts of Lactobacillus (p?<?0.01) and decreased the counts of Enterococcus (p?<?0.01) and Clostridium (p?<?0.05) in the jejunum, whereas the counts of Blautia were increased (p?<?0.01) and Enterococcus were decreased (p?<?0.05) in the cecum at both ages. Only minor CMB effects were identified in the cecum and non in the jejunum. The use of CTS dietary supplements has been shown to be associated to the reduction of potentially pathogenic bacteria (Enterococcus and Clostridium) and to the growth of beneficial bacteria (Lactobacillus and Blautia) which are known to have positive effects on chicken health in terms of nutrients absorption, stimulation and production of short chain fatty acids (SCFAs). Therefore, this study suggests that the use of a CTS supplemented diet could promote gut health while no clear advantages have been identified with the use of CMB as a dietary supplement.

Effects of rearing systems (cage versus floor) on the microbial composition and transcriptome of goose ileum

There is a gradual transition from water to dryland rearing of geese. In this study, we performed 16S rRNA sequencing (16S rRNA-seq) and transcriptome sequencing (RNA-seq) to reveal the effects of cage rearing (CR) and floor rearing (FR) systems on the microbial composition and transcriptome of the goose ileum. Through 16S rRNA-seq, Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 2 (hgcI_clade and Faecalibacterium) and 14 (Bacteroides, Proteiniphilum, Proteiniclasticum, etc.) differential microbiota in CR and FR, respectively. The rearing system influenced 4 pathways including biosynthesis of amino acids in ileal microbiota. Moreover, we identified 1,198 differentially expressed genes (DEGs) in the ileum mucosa, with 957 genes up-regulated in CR and 241 genes up-regulated in FR. In CR, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the significant enrichment (p &amp;lt; 0.05) of 28 KEGG pathways, most of which were associated with amino acid metabolism. In FR, up-regulated DEGs were mainly enriched in KEGG pathways associated with cellular processes, including apoptosis, necroptosis, and cellular senescence. Spearman correlation analysis of differential microbiota and amino acid metabolism-related DEGs in CR showed a significant positive correlation. Additionally, differential microbiota of FR, Phascolarctobacterium and Sutterella, were positively correlated with FGF10 (p &amp;lt; 0.05) and PIK3R1 (p &amp;lt; 0.01), respectively. In conclusion, there might be differences in ileal amino acid metabolism levels between CR and FR geese, and the observed increase in harmful bacterial species in FR might impact the activity of ileal cells.

#2227 Exploring the interplay between gut microbiome, fecal metabolomics and ambulatory blood pressure in white-coat hypertensive patients

Abstract Background and Aims Recent evidence showed the relationship between gut microbiota with hypertension. Few studies also demonstrated that ambulatory blood pressure monitoring variables such as dipping status and linear variability are associated with fecal microbiota and metabolomics. However, the relationship between gut microbiota and metabolomic composition of white-coat hypertensive patients has not been studied yet. In addition, although the link between gut microbiota, blood pressure variability and high salt intake has been shown, none of the studies addressed these changes simultaneously in the same study population. Here, we aimed to investigate the interplay between the gut microbiome, fecal metabolites and 24-hour urine sodium levels between hypertensive, white-coat hypertensive (WCH) and healthy participants diagnosed with ambulatory blood pressure monitoring. Method The study included 18 newly diagnosed hypertensive, 8 WCH, and 21 healthy participants from our tertiary center. Ambulatory blood pressure (BP) monitoring was performed in all participants and nighttime dipping, morning BP surge (MBPS), pre-wake MBPS and linear BP variability were calculated. 16S rRNA sequencing was performed using Illumina MiSeq sequencer. DeSeq2 and linear discriminant analysis effect size (LEfSe) were performed with R. Fecal metabolite levels were analyzed by GC-MS. A partial least squares-discriminant analysis (PLS-DA) model was constructed for the feature selector and classifier. The variable importance in the projection (VIP) coefficient was calculated based on the PLS-DA model. Results ANOVA and post-hoc Tukey test showed WHC and hypertensive groups had higher blood pressure variability and morning-thorough MBPS than normotensive patients (p = 0.02 and 0.04, respectively), whereas 24-h urine Na levels were statistically similar between WCH and hypertensive groups (p = 0.11). There were no significant differences in α- and β-diversity metrics of gut microbiome between study groups. Select taxa were specific to WHC patients, notably Rikenellaceae family and Mitsuokella were higher in WHC against normotensive patients, whereas Ruminococcus callidus, Roseburia, Clostridium, Lactobacillus ruminis, Sutterall, Lachospiraceae and Muribaculaceae were decreased in WHC against normotensive patients in DeSeq2 analysis. Dialister was increased, whereas Bacteroides genus and Bacteroides fragilis were decreased in WHC against hypertensive patients. LEfSe analysis showed positive enrichment in Proteobacteria phylum and negative enrichment in Mitsuokella genus in WHC against hypertensive group. Enterococcus, Lachnobacterium, Odoribacter and Pseudomonas genera had positive; whereas Lactobacillus and Clostridium had negative correlations with 24-h urine Na levels. Positive correlations were shown between linear BP variability and Bacteroides and Paraprevotella genera. Several genera and species were enriched in Q3-4 against Q1-2 quartiles of pre-wake and sleep-thorough MBPS in LEfSe analyzes (Fig. 1). Normotensive and essential hypertensive groups could also be differentiated based on fecal metabolomic composition. Specifically, metabolites with the highest VIP values discriminating WCH from normotensive and hypertensive groups were methyl-palmitoleate, oxalic acid and phenyl β-D-glucopyranoside, respectively (Fig. 2). Conclusion In conclusion, we performed the first study focusing on the fecal microbiome and metabolomic characteristics of white-coat hypertensive patients. Urine Na levels and ambulatory blood pressure variables of the WCH group are different than those of the normotensive and similar to the hypertensive group. Comparative and correlation analyses revealed novel relationships between ambulatory blood pressure variables and gut microbiome of both WCH and hypertensive patients. Fecal metabolomic differences between study groups imply possible mechanisms underlying the effects of gut microbiome on blood pressure. Gut microbiota and metabolites may become valuable targets for interventions of both white-coat and essential hypertension in the near future.

Revealing microbial community composition and disinfection efficacy evaluation in wholesale pork markets through 16S rDNA sequencing

ABSTRACT This study has employed 16S rDNA analysis to elucidate the characteristics of the microbial community in the surroundings, facilities, and meat samples collected from a pork wholesale market with the aim of revealing bacterial contamination. In addition, the efficacy of sodium hypochlorite disinfectant was assessed by comparing the bacterial communities in the viable samples before and after disinfection. The bacterial abundances in meat, chopping boards, and knives were positively correlated (r > 0.95, p < .05), suggesting potential cross-contamination risks during market transactions. The species richness indices for the external transport vehicles, pork hooks, and floors were significantly different from those of the samples taken after decontamination (p < .05). Linear discriminant analysis Effect Size (LEfSe) analyses showed that Firmicutes, Proteobacteria, and Chloroflexi were significantly more abundant in the transaction period, whereas Bacteroidetes levels decreased compared to the clean-up period. NaClO disinfection altered the composition of bacterial communities.

Comparison of the sputum microbiome between patients with stable nontuberculous mycobacterial pulmonary disease and patients requiring treatment.

We evaluated whether the sputum bacterial microbiome differs between nontuberculous mycobacteria pulmonary disease (NTM-PD) patients with stable disease not requiring antibiotic treatment and those requiring antibiotics. We collected sputum samples from 21 clinically stable NTM-PD patients (stable group) and 14 NTM-PD patients needing antibiotic treatment (treatment group). We also obtained 13 follow-up samples from the stable group. We analyzed the 48 samples using 16S rRNA gene sequencing (V3-V4 region) and compared the groups. In the linear discriminant analysis effect size (LEfSe) analysis, the species Porphyromonas pasteri, Haemophilus parahaemolyticus, Prevotella nanceiensis, and Gemella haemolysans were significantly more prevalent in the sputum of the stable group compared to the treatment group. No taxa showed significant differences in alpha-/beta-diversity or LEfSe between the 21 baseline and 13 follow-up sputum samples in the stable group. In the stable group, the genus Bergeyella and species Prevotella oris were less common in patients who achieved spontaneous culture conversion (n = 9) compared to those with persistent NTM positivity (n = 12) (effect size 3.04, p = 0.039 for Bergeyella; effect size 3.64, p = 0.033 for P. oris). In the treatment group, H. parainfluenzae was more common in patients with treatment success (n = 7) than in treatment-refractory patients (n = 7) (effect size 4.74, p = 0.013). Our study identified distinct bacterial taxa in the sputum of NTM-PD patients based on disease status. These results suggest the presence of a microbial environment that helps maintain disease stability.

Analysis of the intestinal microbiota and profiles of blood amino acids and acylcarnitines in neonates with hyperbilirubinemia

ObjectiveThis study aimed to discuss the distinctive features of the intestinal microbiota in neonates with hyperbilirubinemia and to comprehensively analyse the composition of the intestinal microbiota as well as the levels of free amino acids and acylcarnitines in the peripheral blood of neonates experiencing hyperbilirubinemia.ResultsAt the phylum level, Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Chloroflexi were the five predominant microbial groups identified in both the hyperbilirubinemia and control groups. Alpha diversity analysis, encompassing seven indices, showed no statistically significant differences between the two groups. However, Beta diversity analysis revealed a significant difference in intestinal microbiota structure between the groups. Linear discriminant analysis effect size (LEfSe) indicated a significant reduction in the abundance of Gammaproteobacteria and Enterobacteriaceae within the hyperbilirubinemia group compared to that in the control group. The heatmap revealed that the control group exhibited increased abundances of Escherichia and Bifidobacterium, while the hyperbilirubinemia group exhibited increased levels of Enterococcus and Streptococcus. Regarding blood amino acids and acylcarnitines, there were greater concentrations of citrulline (Cit), arginine (Arg), ornithine (Orn), and valine (Val) in the hyperbilirubinemia group than in the control group. The hyperbilirubinemia group also exhibited significant increases in medium-chain fatty acids (C6, C8), long-chain fatty acids (C18), and free carnitine (C0).ConclusionBy comparing neonates with hyperbilirubinemia to those without, a significant disparity in the community structure of the intestinal microbiota was observed. The intestinal microbiota plays a crucial role in the bilirubin metabolism process. The intestinal microbiota of neonates with hyperbilirubinemia exhibited a certain degree of dysbiosis. The abundances of Bacteroides and Bifidobacterium were negatively correlated with the bilirubin concentration. Therefore, the fact that neonates with hyperbilirubinemia exhibit some variations in blood amino acid and acylcarnitine levels may provide, to a certain degree, a theoretical basis for clinical treatment and diagnosis.

Third-generation PacBio sequencing to explore gut bacteria and gender in colorectal cancer

BackgroundGut bacteria have an important influence on colorectal cancer (CRC). The differences of gut bacteria between genders have been the hot spots. ObjectiveTo analyze the relationship between gut bacteria and gender differences in patients with CRC. MethodsA total of 212 patients with CRC and 212 healthy volunteers were recruited. The subjects' fecal samples were obtained, and the fecal microorganisms were analyzed by the third-generation sequencing PacBio. The composition of gut bacteria was analyzed. Linear discriminant analysis Effect Size (LEfSe) was used to analyze the differences in gut bacteria. Pearson coefficient was used to calculate the correlation between differential bacteria. CRC risk prediction models were used to rank the importance of effective differential bacteria. ResultsEscherichia flexneri and Phocaeicola vulgatus were the most frequent bacteria in both male and female CRC patients. Bacteroides, Verrucomicrobia and Akkermansiaceae were highly enriched in male CRC group, while Bacteroidetes, Phocaeicola and Tissierellales were highly enriched in female CRC group. Peptostreptococcus anaerobius and Phocaeicola vulgatus were important CRC related bacteria in males and females, respectively. Peptostreptococcus anaerobius was the most important characteristic bacterium of males (AUC = 0.951), and the sensitivity and specificity of the discovery set were 78.74 % and 93.98 %, respectively. Blautia stercoris was the most important characteristic bacterium of females (AUC = 0.966), and the sensitivity and specificity of the discovery set were 90.63 % and 90.63 %, respectively. ConclusionGut bacteria varied in different genders. Therefore, gender should be considered when gut bacteria are applied in the diagnose and prevention of CRC.

Profiles of Circulating Exosomal Mirna in Patients with SAPHO Patients by High-Throughput Sequencing.

Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome is a rare disease that is characterized by autoinflammatory lesions on both bones and skin. The diverse manifestations and limited understanding of its etiology have hindered the diagnosis and treatment of this condition. SAPHO syndrome is also classified as a primary inflammatory osteitis. The onset of osteoarticular involvement in this disease is typically gradual, and the identification of associated biomarkers may be crucial for accurate diagnosis, effective treatment, and a better understanding of its underlying mechanisms. We enrolled a total of 6 SAPHO patients and 3 healthy volunteers for this study. The miRNA expression profile in circulating exosomes was analyzed using next-generation sequencing. A total of 45 miRNAs were found to be differentially expressed in SAPHO patients. Linear discriminant analysis effect size analysis and Wilcoxon rank-sum test were employed to identify biomarkers based on these differentially expressed miRNAs. Among them, we selected 4 miRNAs as biomarkers for SAPHO syndrome, resulting in an area under the receiver operating characteristic curve of 1. The differentially expressed miRNAs indicated enrichment in immune system and endocrine system-related KEGG pathways, as well as infectious diseases and cancers. Furthermore, the most significantly enriched molecular functions in GO analysis were protein binding and catalytic activity. The exosomal miRNA profile in SAPHO syndrome exhibited significant changes, suggesting its potential as a candidate biomarker for diagnostic assistance, although further investigation is warranted to elucidate their role in the pathology.

Characterization and functional prediction of the dental plaque microbiome in patients with alveolar clefts.

Alveolar cleft (AC) is a common congenital defect in people with cleft lip and palate (CLP). Alveolar bone grafting (ABG) is typically performed during adolescence, resulting in the fissure remaining in the mouth for a longer length of time. Patients with AC have a greater rate of oral diseases such as dental caries than the normal population, and the precise characteristics of the bacterial alterations caused by AC are unknown. We recruited a total of 87 subjects and collected dental plaque samples from AC adolescents (AAP), post-operative ABG adolescents (PAP), healthy control adolescents (CAP), AC young adults (AYP), post-operative ABG young adults (PYP), and healthy control young adults (CYP). The sequencing of 16S rRNA genes was performed. The microbial composition of plaque from alveolar cleft patients differed significantly from age-matched healthy controls. Linear discriminant analysis effect size (LEfSe) analysis revealed that AAP was enriched for Neisseria, Haemophilus, Fusobacterium, Rhodococcus, Aggregatibacter, Gemella, and Porphyromonas, whereas AYP was enriched for Capnocytophaga, Rhodococcus, and Actinomyces-f0332. There were phenotypic differences in facultatively anaerobic, Gram-negative, Gram-positive, and oxidative stress tolerance between the AYP group with longer alveolar cleft and the healthy control group according to Bugbase phenotypic predictions. Alveolar bone grafting did not alter the functional phenotype of alveolar cleft patients but reduced the number of differential genera between alveolar cleft patients and healthy controls at both ages. Our study systematically characterized the supragingival plaque microbiota of alveolar cleft patients, post-alveolar bone grafting patients, and matched healthy controls in two ages to gain a better understanding of plaque ecology and microbiology associated with alveolar clefts.

Beneficial changes in gut microbiota after phototherapy for neonatal hyperbilirubinemia.

Phototherapy is the most commonly used treatment for neonatal hyperbilirubinemia (NH). Gut microbiota is involved in bilirubin metabolism; however, it is uncertain whether this is affected by phototherapy. The present study included 43 newborns with hyperbilirubinemia and collected fecal samples for high-throughput sequencing before and after phototherapy. Selection α diversity analysis was used to determine the differences in diversity and abundance between the two groups, whereas similarity was determined using β diversity analysis. Linear discriminant analysis effect size analysis was used to screen for markedly different bacteria. The structure of the gut microbiota in newborns with hyperbilirubinemia changed after phototherapy, with a significant decrease in abundance and diversity. The changes in the key bacterial species were characterized by an increase in the abundance of Streptococcus salivarius and a decrease in the abundance of Escherichia, Klebsiella pneumoniae, Rothia mucilaginosa and Streptococcus oralis. These changes mainly manifested as an increase in beneficial bacteria and a decrease in opportunistic bacteria, which may not be related to the side effects of phototherapy. These results can provide theoretical assistance for microbiological research on the later stages of NH.

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Industrial farming is one of the main farming systems used for L. vannamei, and it is also the main direction of development in the future. To investigate the role of the bacterial community in nitrogen transformation in industrial L. vannamei farming systems, we studied the concentration of nitrogen compounds, the bacterial community using 16S rRNA sequencing, and nitrogen cycling genes’ abundance using absolute quantitative PCR in aquaculture water (using seawater (WD) and groundwater mixed with seawater (CY)) and analyzed the correlations between them using a person analysis. The results showed that the bacterial α-diversity index (ACE, Shannon, and Sobs) significantly changed during culture in WD but not in CY. Bacterial community species composition analysis and linear discriminant analysis effect size (LEfSe analysis) revealed that Cyanobiaceae and Microbacteriaceae were the dominant bacteria and biomarkers in WD. Vibrionaceae, Ateromonadaceae, Microbacteriaceae, Saprospiraceae, and Cryomorphaceae were the dominant bacteria and biomarkers in CY. A functional annotation of procaryotic taxa (FAPROTAX) analysis revealed that the bacterial community in WD exhibited a greater phototrophic activity at early culture stages, while at the same stage, CY exhibited strong nitrate reduction. A correlation analysis of nitrogen cycling genes and environmental factors revealed that napA, narG, ureC, amoA, and nirK were significantly correlated with the concentrations of total ammonia nitrogen (TAN), nitrite (NO2−-N), nitrate (NO3−-N), and total nitrogen (TN) in WD. In CY, amoA was positively correlated and napA and nirK were negatively correlated with TAN and TN concentrations. A correlation analysis between bacterial abundance and environmental factors revealed that Flavobacteriaceae, Saprospiraceae, Cryomorphaceae, Cyanobiaceae, Halieaceae, and Cyclobacteriaceae were significantly correlated with the concentrations of TAN and NO2−-N. The above results indicated that the bacterial community in industrial shrimp farming systems changed under different conditions, with consequent changes in the abundance of genes being involved in the nitrogen cycle and in this biogeochemical process in the water. Our study facilitates further understanding of microbes and their functions in nitrogen cycling in industrial shrimp farming systems.

Effects of herbal dregs supplementation of Salvia miltiorrhiza and Isatidis Radix residues improved production performance and gut microbiota abundance in late-phase laying hens.

The present study was designed to evaluate the effect of a mixture of Chinese medicinal residues (CMRs) consisting of Salvia miltiorrhiza residues (SMR) and Isatidis Radix residues (IRR) on productive performance, egg quality, serum lipid and hormone levels, liver and blood antioxidant capacity, oviduct inflammation levels, and gut microbiota in the late-laying stage. A total of 288 fifty-four-week-old BaShang long-tailed hens were divided into four groups. The feed trial period was 8 weeks. The control group was fed the basic diet as a CCMR group, supplemented with 3, 4, and 6% for the experimental groups LCMR, MCMR, and HCMR. The egg production rate of the MCMR group was 8.1% higher than that of the CCMR group (p < 0.05). Serum triglyceride (TG) levels of hens of the CMR-supplemented group were significantly decreased than those of the CCMR group (p < 0.05). The group supplemented with different levels of CMR had significantly higher serum HDL-C levels compared with the control group (p < 0.05). Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels were remarkably increased for the LCMR and MCMR groups and significantly decreased for the HCMR group compared to CCMR (p < 0.05). Serum and liver glutathione peroxidase (GSH-PX) activities were significantly increased, and malondialdehyde (MDA) levels were significantly decreased in the MCMR group compared to the CCMR group (p < 0.05). The expression levels of tubal inflammatory factor markers (IL-4, IL-1β, TNF-α) in the MCMR and HCMR groups were consistent with the pathological findings of the sections. As for cecal microbiota, supplementation with CMR affected the alpha diversity of the cecum microbiome at the genus level. The Shannon index was significantly higher in the MCMR group than in the CCMR and HCMR groups (p < 0.05). Supplementation with different levels of CMR mainly regulated the ratio of intestinal Firmicutes to Bacteroidetes and the abundance of phyla such as Proteobacteria. In addition, CMR supplementation at different levels in the diet enriched lipid-metabolizing bacteria, such as Bacteroides and Ruminococcus_gnavus_group. Furthermore, according to linear discriminant analysis (LDA) effect size (LEfSe) analysis, the MCMR group showed an increase in the number of short-chain fatty acid-producing bacteria Romboutsia and fiber-degrading specialized bacteria Monoglobus. Therefore, supplementation of appropriate amounts of CMR to the diet of laying hens enhanced reproductive hormone levels, hepatic antioxidant capacity, and lipid metabolism, alleviated the levels of oviductal inflammatory factors, and modulated the abundance structure of bacterial flora to improve the late-laying performance and egg quality. The results of the current study showed that CMR is a beneficial feed supplement for chickens when added in moderation.

Integrative analyses identify opportunistic pathogens of patients with lower respiratory tract infections based on metagenomic next-generation sequencing

Lower respiratory tract infections (LRTIs) represent some of the most globally prevalent and detrimental diseases. Metagenomic next-generation sequencing (mNGS) technology has effectively addressed the requirement for the diagnosis of clinical infectious diseases. This study aimed at identifying and classifying opportunistic pathogens from the respiratory tract-colonizing microflora in LRTI patients using data acquired from mNGS analyses. A retrospective study was performed employing the mNGS data pertaining to the respiratory samples derived from 394 LRTIs patients. Linear discriminant analysis effect size (LEfSe) analysis was conducted to discern the discriminant bacteria. Receiver operating characteristic curves (ROC) were established to demonstrate discriminant bacterial behavior to distinguish colonization from infection. A total of 443 discriminant bacteria were identified and segregated into three cohorts contingent upon their correlation profiles, detection frequency, and relative abundance in order to distinguish pathogens from colonizing microflora. Among them, 119 emerging opportunistic pathogens (cohort 2) occupied an average area under the curve (AUC) of 0.976 for exhibiting the most prominent predictability in distinguishing colonization from infection, 39 were colonizing bacteria (cohort 1, 0.961), and 285 were rare opportunistic pathogens (cohort 3, 0.887). The LTRIs patients appeared modular in the form of cohorts depicting complex microbial co-occurrence networks, reduced diversity, and a high degree of antagonistic interactions in the respiratory tract microbiome. The study findings indicate that therapeutic interventions should target interaction networks rather than individual microbes, providing an innovative perspective for comprehending and combating respiratory infections. Conclusively, this study reports a profile of LRTIs-associated bacterial colonization and opportunistic pathogens in a relatively large-scale cohort, which might serve as a reference panel for the interpretation of mNGS results in clinical practice.

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.

Microbial community structure and carbon transformation characteristics of different aggregates in black soil.

Previous research on whole-soil measurements has failed to explain the spatial distribution of soil carbon transformations, which is essential for a precise understanding of the microorganisms responsible for carbon transformations. The microorganisms involved in the transformation of soil carbon were investigated at the microscopic scale by combining 16S rDNA sequencing technology with particle-level soil classification. In this experiment,16S rDNA sequencing analysis was used to evaluate the variations in the microbial community structure of different aggregates in no-tillage black soil. The prokaryotic microorganisms involved in carbon transformation were measured before and after the freezing and thawing of various aggregates in no-tillage black soil. Each sample was divided into six categories based on aggregate grain size: >5, 2-5, 1-2, 0.5-1, 0.25-0.5, <0.25 mm, and bulk soil. The relative abundance of Actinobacteria phylum in <0.25 mm aggregates was significantly higher compared to that in other aggregates. The Chao1 index, Shannon index, and phylogenetic diversity (PD) whole tree index of <0.25 mm aggregates were significantly smaller than those of in bulk soil and >5 mm aggregates. Orthogonal partial least-squares discrimination analysis showed that the microbial community composition of black soil aggregates was significantly different between <1 and >1 mm. The redundancy analysis (RDA) showed that the organic carbon conversion rate of 0.25-0.5 mm agglomerates had a significantly greater effect on their bacterial community structure. Moreover, humic acid conversion rates on aggregates <0.5 mm had a greater impact on community structure. The linear discriminant analysis effect size (LEfSe) analysis and RDA analysis were combined. Bradyrhizobium, Actinoplane, Streptomyces, Dactylosporangium, Yonghaparkia, Fleivirga, and Xiangella in <0.25 mm aggregates were positively correlated with soil organic carbon conversion rates. Blastococcus and Pseudarthrobacter were positively correlated with soil organic carbon conversion rates in 0.25-0.5 mm aggregates. In aggregates smaller than 1 mm, the higher the abundance of functional bacteria that contributed to the soil's ability to fix carbon and nitrogen. There were large differences in prokaryotic microbial community composition between <1 and >1 mm aggregates. The <1 mm aggregates play an important role in soil carbon transformation and carbon fixation. The 0.25-0.5 mm aggregates had the fastest organic carbon conversion rate and increased significantly more than the other aggregates. Some genus or species of Actinobacteria and Proteobacteria play a positive role in the carbon transformation of <1 mm aggregates. Such analyses may help to identify microbial partners that play an important role in carbon transformation at the micro scale of no-till black soils.

Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease.

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.