Linear Discriminant Analysis Effect Size Research Articles

Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy.

Children diagnosed with severe tonsillar hypertrophy display discernible craniofacial features distinct from those with adenoid hypertrophy, prompting illuminating considerations regarding microbiota regulation in this non-inflammatory condition. The present study aimed to characterize the salivary microbial profile in children with tonsillar hypertrophy and explore the potential functionality therein. A total of 112 children, with a mean age of 7.79 ± 2.41 years, were enrolled and divided into the tonsillar hypertrophy (TH) group (n = 46, 8.4 ± 2.5 years old), adenoid hypertrophy (AH) group (n = 21, 7.6 ± 2.8 years old), adenotonsillar hypertrophy (ATH) group (n = 23, 7.2 ± 2.1 years old), and control group (n = 22, 8.6 ± 2.1 years old). Unstimulated saliva samples were collected, and microbial profiles were analyzed by 16S rRNA sequencing of V3-V4 regions. Diversity and composition of salivary microbiome and the correlation with parameters of overnight polysomnography and complete blood count were investigated. As a result, children with tonsillar hypertrophy had significantly higher α-diversity indices (P＜0.05). β-diversity based on Bray-Curtis distance revealed that the salivary microbiome of the tonsillar hypertrophy group had a slight separation from the other three groups (P＜0.05). The linear discriminant analysis effect size (LEfSe) analysis indicated that Gemella was most closely related to tonsillar hypertrophy, and higher abundance of Gemella, Parvimonas, Dialister, and Lactobacillus may reflect an active state of immune regulation. Meanwhile, children with different degrees of tonsillar hypertrophy shared similar salivary microbiome diversity. This study demonstrated that the salivary microbiome in pediatric tonsillar hypertrophy patients had different signatures, highlighting that the site of upper airway obstruction primarily influences the salivary microbiome rather than hypertrophy severity.IMPORTANCETonsillar hypertrophy is the most frequent cause of upper airway obstruction and one of the primary risk factors for pediatric obstructive sleep apnea (OSA). Studies have discovered that children with isolated tonsillar hypertrophy exhibit different craniofacial morphology features compared with those with isolated adenoid hypertrophy or adenotonsillar hypertrophy. Furthermore, characteristic salivary microbiota from children with OSA compared with healthy children has been identified in our previous research. However, few studies provided insight into the relationship between the different sites of upper airway obstruction resulting from the enlargement of pharyngeal lymphoid tissue at different sites and the alterations in the microbiome. Here, to investigate the differences in the salivary microbiome of children with tonsillar hypertrophy and/or adenoid hypertrophy, we conducted a cross-sectional study and depicted the unique microbiome profile of pediatric tonsillar hypertrophy, which was mainly characterized by a significantly higher abundance of genera belonging to phyla Firmicutes and certain bacteria involving in the immune response in tonsillar hypertrophy, offering novel perspectives for future related research.

PSIII-12 Dynamics of neonatal dairy calf behaviors and their association with early gut microbiota

Abstract The behavior of dairy cattle can be both an indicator and a determinant of their productivity and health. Additionally, animal behavior is also associated with their gastrointestinal microbiota through the bi-directional pathways of the gut-brain axis, influencing nutrient utilization and gut health. Few studies have looked at the dynamics of neonatal calf behaviors and their associations with early microbiota development. Therefore, the objective of this study is to observe feeding behaviors and activity of neonatal dairy calves and investigate its associations with the diversity and composition of early-stage gut microbiota. We used Holstein-Angus crossed calves (n = 25) raised in individual outdoor hutches and bucket-fed milk replacer twice daily. The number of milk exposures until calves were successfully bucket trained was recorded, along with milk consumption times during the AM feedings on d 7, 11, and 14. We also monitored the activity of the calves using HOBO Pendant G Data Logger accelerometers secured on the right hind leg of each calf to monitor standing and lying behavior from d 3 to d 13. Fecal samples were collected from the recto-anal junction of the calves at d 7 and 14 after birth and gut microbiota were analyzed using full-length 16S rRNA gene amplicon sequencing on an Oxford Nanopore sequencer. The Generalized Linear Model (GLM) was applied to evaluate effects of gender and birth weight on behavior and gut microbiota using RStudio 4.2.1. The Linear discriminant analysis Effect Size (LEfSe) was used to determine the unique bacterial species for each behavioral group. The results revealed that there was no influence of sex or birth weight on bucket training or consumption time; however, male calves exhibited significantly increased total standing time compared with female calves. We found no significant difference in microbiota between fast-learning calves (one milk exposure; n = 3) and slow-learning calves (5 or more exposures; n = 3). We observed greater alpha diversity of slow drinking calves (top 25%; n = 6) compared with fast drinking calves (top 25%; n = 6) on d 7 (Chao1; P = 0.03). The LEfSe analysis identified Akkermansia muciniphilia to be more abundant in fast drinking calves, and Megasphaera elsdenii to be more abundant in slow drinking calves. Additionally, a trend of differing microbiota composition was observed between the most active and least active calves (n = 4 per group) on d 14 (Bray-Curtis; P = 0.1), and many Prevotella species were more abundant in the most active calves. In conclusion, this study sheds light on the gut-brain axis of neonatal dairy calves at the species-level and provides further insights into cognitive, consumptive, and active behaviors.

From Skin to Gut: Understanding Microbial Diversity in Rana amurensis and R. dybowskii.

Amphibians face the threat of decline and extinction, and their health is crucially affected by the microbiota. Their health and ecological adaptability essentially depend on the diverse microbial communities that are shaped by unique host traits and environmental factors. However, there is still limited research on this topic. In this study, cutaneous (C) and gut (G) microbiota in Rana amurensis (A) and R. dybowskii (D) was analyzed through 16S amplicon sequencing. Groups AC and DC significantly differed in alpha diversity, while the gut groups (AG and DG) showed no such differences. Analyses of Bray-Curtis dissimilarity matrix and unweighted UniFrac distances showed significant differences in cutaneous microbiota between groups AC and DC, but not between groups AG and DG. Stochastic processes significantly influenced the assembly of cutaneous and gut microbiota in amphibians, with a notably higher species dispersal rate in the gut. The predominant phyla in the skin of R. amurensis and R. dybowskii were Bacteroidetes and Proteobacteria, respectively, with significant variations in Bacteroidota. Contrarily, the gut microbiota of both species was dominated by Firmicutes, Proteobacteria, and Bacteroidetes, without significant phylum-level differences. Linear discriminant analysis effect size (LEfSe) analysis identified distinct microbial enrichment in each group. Predictive analysis using phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) revealed the significant functional pathways associated with the microbiota, which indicates their potential roles in immune system function, development, regeneration, and response to infectious diseases. This research underscores the critical impact of both host and environmental factors in shaping amphibian microbial ecosystems and emphasizes the need for further studies to explore these complex interactions for conservation efforts.

187 Exploring deep shotgun sequencing to understand the rumen microbial function in Angus bulls with divergent RFI EPD

Abstract We investigated the rumen microbiome of Angus bulls selected for Residual Feed Intake-Expected Progeny Difference (RFI-EPD) utilizing deep shotgun metagenomic sequencing. Negative RFI-EPD bulls (NegRFI: n = 10; RFI-EPD = -0.3883 kg/d) and Positive RFI-EPD bulls (PosRFI: n = 10; RFI-EPD = 0.2935 kg/d) were selected from a group of 59 Angus bulls [average body weight (BW) = 427.81 ± 18.77 kg] fed a high-forage total mixed ration after a 59-d testing period. At the end of the 59-d period, rumen fluid samples were collected for bacterial DNA extraction and subsequent shotgun metagenomic sequencing. Results of the metagenome analysis revealed greater gene richness in NegRFI bulls compared with PosRFI. Analysis of similarity revealed a significant difference (P = 0.05) in the rumen microbial community between the NegRFI and PosRFI. Linear Discriminant Analysis effect size (Lefse) was used to identify the differentially abundant taxa. The Lefse results showed that class Fibrobacteria (LDA = 5.1) and genus Fibrobacter (LDA = 4.8) were the most differentially enriched markers in NegRFI bulls, compared with PosRFI bulls. Relative abundance of the carbohydrate-active enzymes was also compared using lefse analysis. The results showed greater relative abundance of glycoside hydrolases and carbohydrate-binding modules such as GH5, CBM86, CBM35, GH43, and CBM6 (LDA > 3.0) in NegRFI bulls whereas GH13 and GT2 were greater in PosRFI. The distinct metabolic and microbial profiles observed in NegRFI, compared with PosRFI bulls, characterized by greater gene richness and specific taxa such as Fibrobacter, and variations in carbohydrate-active enzymes, underscore the potential genetic and functional differences in their rumen microbiome. These findings contribute to a deeper understanding of the interplay between host genetics, microbiota, and feed efficiency in Angus bulls, opening avenues for targeted interventions and advancements in livestock management practices.

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

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

Gut microbial and metabolic features associated with Clostridioides difficile infection recurrence in children

Abstract Background Recurrent Clostridioides difficile (C. difficile) infection (rCDI) is a critical clinical issue due to the increase in incidence and difficulty in treatment. We aimed to identify gut microbial and metabolic features associated with disease recurrence in a group of pediatric CDI patients. Methods A total of 84 children with primary CDI were prospectively enrolled in the study. Fecal samples collected at the initial diagnosis were subjected to 16S rRNA gene sequencing and targeted metabolomics analysis to profile the bacterial composition and metabolome. Results Twenty-six (26/84, 31.0%) pediatric CDI patients experienced recurrence. The alpha diversity of the fecal microbiota was significantly lower in the recurrent group than in the nonrecurrent group, and the beta diversity was different from that of the nonrecurrent group. Taxonomic profiles revealed that the relative abundances of multiple bacterial taxa significantly differed between the recurrent and nonrecurrent groups. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified several bacterial genera that discriminated between recurrent and nonrecurrent groups, including Parabacteroides, Coprococcus, Disalister and Clostridium. Recurrent bacteria presented lower abundances of several short-chain fatty acid (SCFA)-producing bacteria (Faecalibacterium, Butyricicoccus, Clostridium, Roseburia, and Ruminococcus), which were correlated with reduced fecal SCFA levels. In addition, several bile acids (BAs), including lithochalic acid (LCA), 12-ketoLCA, trihydroxycholestanoic acid (3-DHCA), and deoxycholic acid (DCA), were decreased in recurrent patients. Conclusions Our study suggests that the differing gut microbiota profiles in pediatric CDI patients may contribute to disease recurrence by modulating SCFA concentrations and BA profiles. The gut microbiota and metabolite signatures may be used to predict disease recurrence in children with CDI.

Differences in the landscape of colonized microorganisms in different oral potentially malignant disorders and squamous cell carcinoma: a multi-group comparative study

BackgroundThe role of microbes in diseases, especially cancer, has garnered significant attention. However, research on the oral microbiota in oral potentially malignant disorders (OPMDs) remains limited. Our study investigates microbial communities in OPMDs.Materials and methodsOral biopsies from19 oral leukoplakia (OLK) patients, 19 proliferative verrucous leukoplakia (PVL) patients, 19 oral lichen planus (OLP) patients, and 19 oral lichenoid lesions (OLL) patients were obtained. 15 SCC specimens were also collected from PVL patients. Healthy individuals served as controls, and DNA was extracted from their paraffin-embedded tissues. 2bRAD-M sequencing generated taxonomic profiles. Alpha and beta diversity analyses, along with Linear Discriminant Analysis effect size analysis, were conducted.ResultsOur results showed the microbial richness and diversity were significantly different among groups, with PVL-SCC resembling controls, while OLK exhibited the highest richness. Each disease group displayed unique microbial compositions, with distinct dominant bacterial species. Noteworthy alterations during PVL-SCC progression included a decline in Fusobacterium periodonticum and an elevation in Prevotella oris.ConclusionsDifferent disease groups exhibited distinct dominant bacterial species and microbial compositions. These findings offer promise in elucidating the underlying mechanisms of this disease.

Characterizing Gut Microbiota in Older Chinese Adults with Cognitive Impairment: A Cross-Sectional Study.

Cognitive impairment is a clinical manifestation that occurs in the course of dementia like Alzheimer's disease. The association between cognitive impairment and gut microbiota is unclear. We aimed to identify gut microbiota characteristics and key gut microbiota biomarkers associated with cognitive impairment in a relatively large cohort of older adults in China. A total of 229 adults aged ≥60 years from Shenzhen, China were recruited into this cross-sectional study. Participants were divided into cognitive impairment (CI) and no cognitive impairment (NCI) groups according to the results of the Mini-Mental State Examination. Diversity analysis and network analysis were used to characterize the gut microbiota between the two groups. The linear discriminant analysis effect size method and machine learning approaches were sequentially performed to identify gut microbiota biomarkers. The relationship between biomarkers and lifestyle factors was explored using Transformation-based redundancy analysis (tb-RDA). A total of 74 CI participants and 131 NCI participants were included in the analysis. The CI group demonstrated lower α-diversity compared to the NCI group (Shannon: 2.798 versus 3.152, p < 0.001). The density of the gut microbiota interaction network was lower in the CI group (0.074) compared to the NCI group (0.081). Megamonas, Blautia, Pseudomonas, Stenotrophomonas, and Veillonella were key biomarkers for CI. The tb-RDA revealed that increased fruit intake and exercise contribute to a higher abundance of Megamonas, Blautia, and Veillonella. We identified a significantly reduced abundance of certain beneficial gut microbiota in older Chinese adults with cognitive impairment.

The effect of oral probiotics in the last trimester on the human milk and infant gut microbiotas at six months postpartum: A randomized controlled trial

ObjectiveThe main aim of this study was to evaluate the effect of oral probiotics on the human milk microbiota and determine whether that influenced infant microbiota development. MethodsA total of 27 pregnant women were recruited; 14 were assigned to the probiotic group, and the rest were assigned to the control group. Their infants were likewise assigned to the probiotic group or the control group. Pregnant women in the probiotic group received probiotic supplementation from 32 weeks of gestation until delivery. Human milk samples and infant fecal samples were collected at 6 months after delivery, and 16S rRNA sequencing was used to analyze the composition of the human milk and infant gut microbiota (NCT06241222). ResultsIn the control group, bacterial microbiota were detected in 8 out of 13 milk samples, whereas in the probiotic group, only 6 out of 14 milk samples contained bacterial microbiota. We examined the composition of the human milk and infant gut microbiota in both the control and probiotic groups. Spearman correlation analysis revealed that various genera in human milk were correlated with the infant gut microbiota. The Linear discriminant analysis effect size (LEfSe) showed that 6 bacteria in the human milk microbiota in the control group were significantly more abundant than those in the probiotic group. Nine bacteria were significantly more abundant in the human milk microbiota in the probiotic group than the control group. According to the LEfSe results, 11 bacteria in the infant gut microbiota in the control group were significantly more abundant than those in the probiotic group. Fourteen bacteria were significantly more abundant in the infant gut microbiota in the probiotic group than in the control group. ConclusionThe infant gut microbiota at 6 months has a complicated relationship with the maternal human milk microbiota. Oral probiotic supplementation can change the composition of the human milk microbiota and the infant gut microbiota.

Advancing fluorescence tracing with 3D-2D spectral conversion: A mixed culture on microbial degradation mechanisms of DOM from a large-scale watershed

Fluorescence tracing, known for its precision, rapid application, and cost-effectiveness, faces challenges due to the microbial degradation of dissolved organic matter (DOM) in aquatic environments, altering its original spectral fingerprint. This study conducted a 15-day microcosm experiment to examine the effects of biodegradation on the spectral properties of DOM from various sources: livestock excrement (EXC), urban sewage (URB), industrial wastewater (IND), and riparian topsoil (tDOM). Our findings show that while the spectral structures of DOM from different sources change during 15 days of microbial degradation, these changes do not overlap or interfere with each other. However, distinguishing between tDOM and URB in the presence of both IND and EXC is only possible at high resolution. Spectral index calculations revealed significant fluctuations and interference in FI and BIX indices among samples from different sources due to microbial degradation. In contrast, the HIX index exhibited independent fluctuations and remained a reliable spectral index for tracing. LEfSe (Linear discriminant analysis Effect Size) identified characteristic bio-indicators (CBI) for each DOM source. The CBI for tDOM and URB differed significantly; tDOM showed a marked CBI only within the first four days of microbial degradation, with a sharp decline in abundance thereafter, while URB's CBI remained abundant for 12 days. Similarly, IND's CBI maintained high relative abundance for the first 12 days. EXC's CBI was unique, showing a distinct and stable community only after six days of degradation, likely due to its high bioavailability and initial rapid microbial utilization. This study addresses the temporal variability in spectral tracing techniques caused by pollutant biodegradation. We developed a combined spectral-biological tracing technique using the “three-dimensional to two-dimensional” method along with bio-indicators, enhancing the accuracy and timeliness of spectral tracing.

Alleviating effects of guar gum on high-fat diet-induced liver injury in common carp (Cyprinus carpio)

This research aimed to determine the effect of dietary guar gum inclusion in high-lipid diets on the liver health of common carp (Cyprinus carpio). Four high-fat diets (10 % crude lipid) containing 0 % (HF), 0.3 % (HFG0.3), 1 % (HFG1), and 3 % (HFG3) of guar gum and a normal-lipid diet (5 % crude lipid; Control) were formulated. The tested diets were evenly and randomly distributed to fifteen tanks, with each tank containing thirty fish (4.53 ± 0.05 g). Fish were fed until apparent satiation for eight weeks. Compared to HF, diets HFG0.3, HFG1, and HFG3 significantly improved feed efficiency, with the HFG0.3 diet enhancing weight gain rate and specific growth rate. The results indicated that HF induced gut dysbiosis, hepatic lipid accumulation, oxidative stress, inflammation, and disturbance in hepatic lipid and cholesterol metabolism. Compared to the HF diet, diets HFG0.3, HFG1, and HFG3 substantially decreased hepatic lipid accumulation and malonaldehyde content, increased catalase activity and the expression of AMP-activated protein kinase (AMPKα2), peroxisomal proliferator-activated receptor alpha (PPARα), cholesterol 7alpha-hydroxylase, and decreased the expression of interleukin-1β (IL-1β). Moreover, the HFG0.3 and HFG1 diets dramatically increased nuclear factor erythroid 2-related factor 2 and liver X receptor expression and decreased protein carbonyl contents and expression of IL-8, nuclear factor kappa B (NF-κB p65), and tumor necrosis factor α. Furthermore, the HFG1 diet significantly increased carnitine palmitoyltransferase 1 and peroxisomal proliferator-activated receptor gamma coactivator 1 expression and reduced expression levels of fibroblast growth factor 19, farnesoid X receptor, and sterol regulatory element-binding protein type 1. The linear discriminant analysis effect size (LEfSe) analysis showed that HFG 0.3 and HFG1 substantially increased the enrichment of beneficial microbiota (e.g., lactic acid bacteria, Cetobacterium, and Fusobacterial) and decreased the enrichment of harmful microbiota (e.g., Proteobacteria, Acinetobacter, and Pseudomonas) compared to HF. These results suggested that guar gum can mitigate high-fat diet-induced liver damage in fish.

Improved Straw Decomposition Products Promote Peanut Growth by Changing Soil Chemical Properties and Microbial Diversity

The ameliorative effects of straw decomposition products on soil acidification have been extensively studied. However, the impact of chemically treated straw decomposition products on crop productivity and the underlying microbial mechanisms remain unclear. This study aimed to investigate the effects of two dosages of Ca(OH)2-treated straw decomposition products of peanuts on red soil acidity, fertility, and bacterial and fungal diversity through a pot experiment. The pot experiment included four treatments: chemical nitrogen, phosphorus, and potassium (NPK) fertilization alone (CK), NPK chemical fertilization combined with peanut straw decomposition products (PS), NPK chemical fertilization combined with 4% Ca(OH)2-treated peanut straw decomposition products (PS4Ca), and NPK chemical fertilization combined with 8% Ca(OH)2-treated straw decomposition products (PS8Ca). High-throughput sequencing was performed to investigate the effects of these treatments on soil microbial diversity. The treatments with PS, PS4Ca, and PS8Ca significantly increased soil pH, exchangeable base cations, and nutrient content, whereas they decreased the exchangeable acid, especially exchangeable aluminum. The peanut growth improved substantially with the application of straw decomposition products. Specifically, PS4Ca significantly increased the Shannon and Richness indices of fungi. The principal coordinate analysis showed that the soil microbial communities in the straw decomposition product treatments were significantly different from CK. Linear discriminant analysis effect size identified unique bacteria and fungi between treatments. The Mantel test indicated that exchangeable base cations and pH were significantly positively correlated with bacterial communities, whereas available potassium was positively correlated with fungal communities. The partial least squares path modeling revealed that the bacterial communities positively and directly affected all peanut agronomic traits. In contrast, the fungal communities had a negative and direct effect only on peanut 100-pod weight. Therefore, adding Ca(OH)2-treated straw decomposition products could effectively improve crop productivity by alleviating soil acidification, increasing soil nutrients, and subsequently changing microorganisms.

A finding of potential coexisting bacteria and characterization of the bacterial communities in the fruiting body of Sarcodon aspratus.

Sarcodon aspratus (Berk.) S. Ito is a Japaneselocal dish with unique aroma and is effective against allergic diseases. However, its cultivation was still difficult. Recently, coexisting bacteria were regarded as an important factor for mycelium growth and fruiting body formation. Therefore, we performed 16S rRNA amplicon sequencing in the fruiting body of S. aspratus and its adhered soil to understand the bacterial communities in the fruiting body of S. aspratus. The fruiting body group showed lower alpha diversities and a significant difference in the structure of bacterial communities compared to the soil group. In addition, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium had the highest relative abundance in the fruiting body group, and it was also a potential coexisting bacterium in the fruiting body of S. aspratus by linear discriminant analysis effect size (LEfSe) analysis. This highest relative abundance phenomenon in Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was also found in the fruiting body of Cantharellus cibarius. These findings suggested that Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium plays a key role in the bacterial communities in the fruiting body of S. aspratus. Bacteria in the fruit bodies of S. aspratus and C. cibarius probably present a similar coexistence model.

Energy reserves and gut microbiota of marine mussels under combined exposure to pathogens and predation risk

In recent years, environmental issues such as eutrophication have led to proliferation of pathogenic bacteria and deterioration of aquaculture environmental water quality. However, the impact of pathogenic bacteria on the mussel-predator food chain in the marine environment is not yet fully understood. In this experiment, mussels were cultured with crabs (Charybdis japonica) for 14 days. Then crabs were retained or removed and pathogenic bacteria (Vibrio alginolyticus) was added and mussels were cultured for 3 days. C. japonica and V. alginolyticus were used as two stressors to explore their effects on energy content and gut microbiota of Mytilus coruscus. The metabolic parameters (protein, carbohydrate and lipid contents) of the gills and digestive glands, and the gut microbiota of the mussels were measured. The study found that presence of predation risk significantly increased the content of protein but decreased carbohydrate and lipid contents in the gills at 14th day. After 17 days of exposure, the presence of predation risk significantly reduced protein content but significantly increased lipid content in gills of mussel. The protein content in digestive gland was significantly increased, but the lipid content was significantly decreased. The presence of predation risk and pathogens had interactive effect on the protein content in the digestive glands of mussels. The presence of V. alginolyticus and predation risk affected the community structure, species richness, and diversity of gut microbiota. The most abundant phyla noted were Bacteroidota, Proteobacteria, and Firmicutes, and the most abundant genus noted were Prevotella, Klebsiella and Dialister. Alpha diversity analysis and beta diversity analysis revealed that the presence of V. alginolyticus and predation risk altered the microbial community structure. V. alginolyticus plays a positive role in the harmful microbiota of gut microbiota. The proportion of Bacteroidota and Proteobacteria in intestinal bacteria increased significantly. Linear discriminant analysis effect size (LEfSe) showed that the biomarkers in each group are significantly different at the genus level. Significant correlations between metabolic parameters (protein content and carbohydrate content) and the level of KEGG function prediction (amino acid metabolism and carbohydrate metabolism) were observed in gills and digestive glands. This study highlights the priority of energy responses in mussels under dual predator-pathogen pressure, and also highlights the complexity of predator-pathogen interactions. A better understanding of their impact on the gut microbiota and health of marine mussels will help support the sustainability of mussel aquaculture production.

Baseline Gut Microbiota Was Associated with Long-Term Immune Response at One Year Following Three Doses of BNT162b2.

This study explored neutralizing IgG antibody levels against COVID-19 decline over time post-vaccination. We conducted this prospective cohort study to investigate the function of gut microbiota in the host immune response following three doses of BNT162b2. Subjects who received three doses of BNT162b2 were recruited from three centers in Hong Kong. Blood samples were obtained before the first dose and at the one-year timepoint for IgG ELISA to determine the level of neutralizing antibody (NAb). The primary outcome was a high immune response (NAb > 600 AU/mL). We performed shotgun DNA metagenomic sequencing on baseline fecal samples to identify bacterial species and metabolic pathways associated with high immune response using linear discriminant analysis effect size analysis. A total of 125 subjects were recruited (median age: 52 years [IQR: 46.2-59.0]; male: 43 [34.4%]), and 20 were regarded as low responders at the one-year timepoint. Streptococcus parasanguinis (log10LDA score = 2.38, p = 0.003; relative abundance of 2.97 × 10-5 vs. 0.03%, p = 0.001), Bacteroides stercoris (log10LDA score = 4.29, p = 0.024; relative abundance of 0.14% vs. 2.40%, p = 0.014) and Haemophilus parainfluenzae (log10LDA score = 2.15, p = 0.022; relative abundance of 0.01% vs. 0, p = 0.010) were enriched in low responders. Bifidobacterium pseudocatenulatum (log10LDA score = 2.99, p = 0.048; relative abundance of 0.09% vs. 0.36%, p = 0.049) and Clostridium leptum (log10LDA score = 2.38, p = 0.014; relative abundance of 1.2 × 10-5% vs. 0, p = 0.044) were enriched in high responders. S. parasanguinis was negatively correlated with the superpathway of pyrimidine ribonucleotides de novo biosynthesis (log10LDA score = 2.63), which contributes to inflammation and antibody production. H. parainfluenzae was positively correlated with pathways related to anti-inflammatory processes, including the superpathway of histidine, purine, and pyrimidine biosynthesis (log10LDA score = 2.14). Among three-dose BNT162b2 recipients, S. parasanguinis, B. stercoris and H. parainfluenzae were associated with poorer immunogenicity at one year, while B. pseudocatenulatum and C. leptum was associated with a better response.

Dynamic changes in and correlations between microbial communities and physicochemical properties during the composting of cattle manure with Penicillium oxalicum

BackgroundPenicillium oxalicum is an important fungal agent in the composting of cattle manure, but the changes that occur in the microbial community, physicochemical factors, and potential functions of microorganisms at different time points are still unclear. To this end, the dynamic changes occurring in the microbial community and physicochemical factors and their correlations during the composting of cattle manure with Penicillium oxalicum were analysed.ResultsThe results showed that the main phyla observed throughout the study period were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Halanaerobiaeota, Apicomplexa and Ascomycota. Linear discriminant analysis effect size (LEfSe) illustrated that Chitinophagales and Eurotiomycetes were biomarker species of bacteria and eukaryote in samples from Days 40 and 35, respectively. Bacterial community composition was significantly correlated with temperature and pH, and eukaryotic microorganism community composition was significantly correlated with moisture content and NH4+-N according to redundancy analysis (RDA). The diversity of the microbial communities changed significantly, especially that of the main pathogenic microorganisms, which showed a decreasing trend or even disappeared after composting.ConclusionsIn conclusion, a combination of high-throughput sequencing and physicochemical analysis was used to identify the drivers of microbial community succession and the composition of functional microbiota during cattle manure composting with Penicillium oxalicum. The results offer a theoretical framework for explaining microecological assembly during cattle manure composting with Penicillium oxalicum.

Taxonomic and functional changes in wheat rhizosphere microbiome caused by imidazoline-based herbicide and genetic modification

Genetically modified (GM) crop cultivation has received a lot of attention in recent years due to the substantial public debate. Consequently, an in-depth investigation of excessively used GM herbicide-tolerant crops is a vital step for the biosafety of genetically modified plants. Several studies have been conducted to study the impact of transgenic GM crops on soil microbial composition; however, research into the effects of non-transgenic GM crops is inadequate. In the current work, high-throughput sequencing was used to evaluate the impact of the acetolactate synthase (ALS)-mutant (WK170B), its control (YN19B), and the imazamox (IM) herbicide on the wheat rhizobiome. Under normal growth conditions, our work revealed a minimal impact of ALS-mutant WK170B on the rhizosphere microbiome compared to the control YN10B, except for some cyanobacterial microorganisms that showed a significant increase in abundance. This suggests that the gene mutation could potentially have a beneficial impact on the bacterial communities present in the rhizosphere. Following IM exposure, taxonomic analysis revealed a significant reduction in the relative abundance of Ralstonia pickettii and an unidentified member of the genus Ancylothrix 8PC. Analyses of both alpha and beta diversity revealed a statistically significant increase in both microbial richness and species diversity. IM-induced relative abundance modulation was also evident through Linear discriminant analysis Effect Size (LEfSe), MetaStat, and heatmap analyses. The SIMPER analysis revealed that the microbial taxa Massilia, Limnobacter, Hydrogenophaga, Ralstonia, Nitrospira, and Ramlibacter exhibited the highest vulnerability to IM exposure. The functional attributes analysis revealed that the relative abundance of genes associated with the extracellular matrix-receptor interaction, which is responsible for structural support and stress response, increased significantly following IM exposure. Collectively, our study identifies key microbial taxa in the wheat rhizobiome that are sensitive to IM herbicides and provides a foundation for assessing the environmental risks associated with IM herbicide use.

Adult Outpatients with Long COVID Infected with SARS-CoV-2 Omicron Variant. Part 1: Oral Microbiota Alterations

BackgroundMany individuals experience long COVID after SARS-CoV-2 infection. As microbiota can influence health, it may change with COVID-19. This study investigated differences in oral microbiota between COVID-19 patients with and without long COVID. MethodsBased on a prospective follow-up investigation, this nested case-control study evaluated the differences in oral microbiota in individuals with and without long COVID (Symptomatic and Asymptomatic groups), which were assessed by 16S rRNA sequencing on tongue coating samples. A predictive model was established using machine learning based on specific differential microbial communities. ResultsOne-hundred-and-eight patients were included (n=54 Symptomatic group). The Symptomatic group had higher Alpha diversity indices (observed_otus, Chao1, Shannon, and Simpson indices), differences in microbial composition (Beta diversity), and microbial dysbiosis with increased diversity and relative abundance of pathogenic bacteria. Marker bacteria (c__Campylobacterota, o__Coriobacteriales, o__Pseudomonadales, and o__Campylobacterales) were associated with long COVID by linear discriminant analysis effect size and receiver operating characteristic curves (AUC 0.821). ConclusionThere were distinct variations in oral microbiota between COVID-19 patients with and without long COVID. Changes in oral microbiota may indicate long COVID.

Wastewater Microbiome Analysis for Population Alcohol Abuse

This study aims to unveil correlations between wastewater microbiota and the catchment-specific population health risk, specifically alcohol abuse, with smoking and obesity as confounding factors. Our study highlights the importance of extracting human-associated microbial communities from wastewater metagenomes by excluding environmental microorganisms, due to their irrelevance to human health. After excluding environmental microbes, we observed strong associations of all three health risk factors, including alcohol abuse, smoking and obesity, with the human gut microbiome in wastewater. The linear discriminant analysis effect size (LEfSe) analysis showed Lactococcus_A, Leuconostoc, Aeromicrobium, Akkermansia, Weissella, Limosilactobacillus, Klebsiella_A, Desulfovibrio and Cloacibacillus as potential microbial biomarkers for alcoholism, after accounting for the confounding effects of smoking and obesity. Functional annotations of microorganisms linked with lower alcoholism rates are primarily related to energy metabolism and intercellular communication. Microorganisms associated with higher alcoholism rates are predominantly involved in immune regulation and cellular DNA architecture. This study highlights the need for a comprehensive exploration of different health risk factors together to identify potential associations between the wastewater microbiome and population lifestyle.

Analysis of blood microbiota in patients with adult-onset Still's disease and sepsis by metagenomic next-generation sequencing.

Aims/Background Adult-onset Still's disease (AOSD) shares similar clinical symptoms with sepsis. Thus, differentiating between AOSD and sepsis presents a great challenge while making diagnosis. This study aimed to analyse the changes in blood microbiota related to AOSD and sepsis using metagenomic next-generation sequencing (mNGS), identify potential biomarkers that distinguish AOSD from sepsis, and explore the diagnostic value of mNGS in differentiation between these two pathological conditions. Methods Clinical data of four AOSD patients and four sepsis patients treated in the Department of Rheumatology and Immunology, The Affiliated Hospital of Xuzhou Medical University between October 2021 and February 2022 were collected. The mNGS diagnostic records of these patients were analysed for microbial correlations in terms of species taxonomic structure and beta diversity by comparing blood microbiota between AOSD and sepsis. The biomarkers with the strongest capability in distinguishing the subgroups were screened using a random forest algorithm. Results There was no statistically significant differences between AOSD patients and sepsis controls in terms of gender and age (p > 0.05). A total of 91 operational taxonomic units (OTUs) were obtained. At the level of phylum, Proteobacteria, Ascomycota and Basidiomycota were present in high abundances in both groups (79.76%, 14.18% and 3.30% vs 54.03%, 32.77% and 5.81%). At the genus level, the abundances of Parainfluenzae, Aspergillus and Ralstonia were the top three highest in the AOSD group (73.88%, 10.92% and 5.48%), while Ralstonia, Aspergillus and Malassezia were ranked as the top three in the sepsis group in term of abundance (48.69%, 27.36% and 5.52%). In beta-diversity analysis, there were advances shown in visual principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) between the AOSD group and sepsis group (p < 0.05), with little significant differences in the analysis of similarities (Anosim) (p > 0.05). Linear discriminant analysis effect size (LEfSe) showed that Mucoromycota, Saccharomycetes, Moraxellales, Mucorales, Xanthomonadales, Saccharomycetales, Acinetobacter, Stenotrophomonas, Yarrowia, Apophysomyces, Acinetobacter johnson, Yarrowia lipolytica, Apophysomyces variabilis and Stenotrophomonas maltophilia were more enriched in sepsis group (p < 0.05). The top five variables with the strongest capability in distinguishing between AOSD and sepsis were Acinetobacter johnsonii, Apophysomyces variabilis, Propionibacterium acnes, Stenotrophomonas maltophilia and Yarrowia lipolytica. Conclusion The blood microorganisms in AOSD were different from sepsis, and mNGS was potential to distinguish between AOSD and sepsis.