Illumina MiSeq Sequencing Research Articles

Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese

Background: Lactiplantibacillus plantarum is a species found in a wide range of ecological niches, including vegetables and dairy products, and it may occur naturally in the human gastrointestinal tract. The precise mechanisms underlying the beneficial properties of these microbes to their host remain obscure. Although Lactic acid bacteria are generally regarded as safe, there are rare cases of the emergence of infections and antibiotic resistance by certain probiotics. Objective: An in silico whole genome sequence analysis of putative probiotic bacteria was set up to identify strains, predict desirable functional properties, and identify potentially detrimental antibiotic resistance and virulence genes. Methods: We characterized the genomes of three L. plantarum strains (54B, 54C, and 55A) isolated from Ethiopian traditional cottage cheese. Whole-genome sequencing was performed using Illumina MiSeq sequencing. The completeness and quality of the genome of L. plantarum strains were assessed through CheckM. Results: Analyses results showed that L. plantarum 54B and 54C are closely related but different strains. The genomes studied did not harbor resistance and virulence factors. They had five classes of carbohydrate-active enzymes with several important functions. Cyclic lactone autoinducer, terpenes, Type III polyketide synthases, ribosomally synthesized and post-translationally modified peptides-like gene clusters, sactipeptides, and all genes required for riboflavin biosynthesis were identified, evidencing their promising probiotic properties. Six bacteriocin-like structures encoding genes were found in the genome of L. plantarum 55A. Conclusions: The lack of resistome and virulome and their previous functional capabilities suggest the potential applicability of these strains in food industries as bio-preservatives and in the prevention and/or treatment of infectious diseases. The results also provide insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates.

Effect of rhizosphere soil microbial communities and environmental factors on growth and the active ingredients of Angelica sinensis in Gansu Province, China.

The growth and accumulation of active ingredients of Angelica sinensis were affected by rhizosphere soil microbial communities and soil environmental factors. However, the correlationship between growth and active ingredients and soil biotic and abiotic factors is still unclear. This study explored rhizosphere soil microbial community structures, soil physicochemical properties, enzyme activities, and their effects on the growth and active ingredient contents of A. sinensis in three principal cropping areas. Results indicated that the growth indices, ligustilide, ferulic acid contents, and soil environmental factors varied in cropping areas. Pearson correlation analysis revealed that the growth of A. sinensis was affected by organic matter, total nitrogen, total phosphorus, and available phosphorus; ferulic acid and ligustilide accumulation were related to soil catalase and alkaline phosphatase activities, respectively. Illumina MiSeq sequencing showed that the genera Mortierella and Conocybe were the dominant fungal communities, and Sphingomonas, Pseudomonas, Bryobacter, and Lysobacter were the main bacterial communities associated with the rhizosphere soil. Kruskal-Wallis one-way ANOVA and Spearman correlation conjoint analysis demonstrated a significant positive correlation (p < 0.001) among the composition of the rhizosphere microbial communities at all three sampling sites. The growth and active ingredient accumulation of A. sinensis not only was significantly susceptible to the bacterial communities of Sphingomonas, Epicoccum, Marivita,Muribaculum, and Gemmatimonas but also were significantly influenced by the fungal communities of Inocybe, Septoria, Tetracladium, and Mortierella (p < 0.05). Our findings provide a scientific basis for understanding the relationship between the growth and active ingredients in A. sinensis and their corresponding rhizosphere soil microbial communities, soil physicochemical properties, and enzyme activities.

Variation in the gut microbiota during the early developmental stages of common carp (Cyprinus carpio L.) and its correlation with feed and pond water microflora

BackgroundFish gut microbiota undergo dynamic changes under the influence of many factors and play an important role in the nutrition, immunity and development in fish. Although common carp (Cyprinus carpio L.) is an economically important freshwater fish, there are few reports on its gut microbiota changes at different early developmental stages. In the present study, the gut microbiota of common carp during the early developmental stages and its correlation with the feed and pond water flora were studied using the Illumina MiSeq sequencing platform.ResultsThe results showed that the gut microbiota of common carp underwent continuous and mild changes over the development process, and the pond water environment might provide bacterial resources and have a certain influence on the changes in the gut microbiota of common carp. However, host selection pressure played a more important role in shaping the gut microbiota. Although the gut microbiota was affected by many factors, the presence of core microbiota indicated that some bacterial species adapt to the gut microenvironment of common carp and played a role in its growth process.ConclusionsThe dynamic changes of gut microbiota of carp in early development stage were related to the feed, water environment and host selection. The results of this study provide a theoretical basis for healthy farming and disease prevention of common carp.

The disturbance of intestinal microbiome caused by the novel duck reovirus infection in Cherry Valley ducklings can induce intestinal damage

Novel duck reovirus disease is an infectious disease mainly caused by novel duck reovirus (NDRV), which is characterized by spleen necrosis and persistent diarrhea in ducks. However, the pathogenic mechanism of NDRV infection in Cherry Valley ducks remains unclear. To investigate the distribution of NDRV in the intestines of Cherry Valley ducks, intestinal morphogenesis, intestinal permeability, inflammatory cytokines, and the expression of tight junction proteins (TJPs), we introduced NDRV via intramuscular infection. The diversity and composition of ileum flora and content of short-chain fatty acids (SCFAs) were analyzed using Illumina MiSeq sequencing. The relationship between changes in the intestinal microbial community and intestinal damage in Cherry Valley ducks infected with NDRV was also assessed to offer new insights into the pathogenesis of NDRV and intestinal flora composition. The results showed that intestinal inflammation and barrier dysfunction occurred following NDRV infection. Additionally, a significant reduction in dominant bacterial species and a decrease in SCFA content within the intestinal microbiota led to weakened colonization resistance and the enrichment of opportunistic pathogens, exacerbating intestinal damage post-NDRV infection. Notably, TJPs and inflammatory cytokine disruptions were linked to a decline in SCFA-producing bacteria and an accumulation of pathogenic bacteria. In summary, changes in the ileum intestinal flora and disruptions to the intestinal barrier were associated with NDRV infection. Consequently, disturbances in intestinal flora caused by NDRV infection can lead to intestinal damage. These findings may offer us a new perspective, targeting the gut microbiota to better understand the progression of NDRV disease and investigate its underlying pathogenesis.

Exploring the Effects of Trichoderma virens Biofungicide on Carrot Cavity Spot and Soil Fungal Community Dynamics

Carrot cavity spot (CCS) has conventionally been managed with fungicides. However, fungicide resistance, their potential risks to human health and the environment, and the increasing demand for organic produce necessitate the exploration of biofungicides as alternatives. In this study, we evaluated varying concentrations of SoilGard (Certis USA, Columbia, MD), a Trichoderma virens-based biofungicide, for efficacy against different CCS-causing Pythium species in vitro. Additionally, its effects on taxonomic and functional diversities of soil fungal communities were studied in vivo in the greenhouse. To our knowledge, this is the first study reporting SoilGard's effectiveness against CCS, with emphasis on its potential as an alternative for fungicide-resistant Pythium isolates. Our in vitro study revealed that SoilGard efficacy was significantly dose-dependent and isolate-specific, thus highlighting the importance of selecting its application rate and the target isolate. Analysis of soil fungal communities using Illumina MiSeq sequencing revealed that SoilGard exerted a significant, albeit temporary, effect on the fungal community structure. It negatively impacted co-occurrence network complexity and alpha diversity in carrot-cultivated soil, whereas bare soil communities remained largely unaffected, thus explaining why preplant applications may yield better results. Our study showed that carrot cultivation without SoilGard enhanced fungal diversity, which was more pronounced late in the season, possibly due to carrot root-associated exudates. Our study sheds light on how complex interactions within soil fungal communities can be impacted by the application of beneficial/pathogenic microbes.

Organic fertilizer significantly mitigates N2O emissions while increase contributed of comammox Nitrospira in paddy soils

Nitrification is the dominant process for nitrous oxide (N2O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N2O production in a range of unfertilized and fertilized paddy soils, using 13CO2-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C2H2), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. 13CO2-DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N2O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N2O emissions. Applying organic fertilizers significantly decreased the N2O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N2O production in other ecosystems than oligotrophic habitats.

The Effects of Brodalumab on the Fungal Microbiome in Patients with Psoriasis.

The gut microbiota plays a critical role in immune system function, with dysbiosis linked to systemic inflammation, contributing to conditions like psoriasis and depression. Although biological treatments for severe psoriasis are known to impact gut bacteria, less is understood about their effects on fungi. This study aims to investigate fungal gut microbiota changes in psoriasis patients transitioning from TNF-α inhibitors to brodalumab. Fecal samples from 20 patients were analyzed using Illumina MiSeq sequencing of the ITS2 region of 18S rRNA. Microbial diversity was assessed through Bray-Curtis dissimilarity and the Shannon-Wiener index. Clinical outcomes were measured using clinical scores for psoriasis and depression severity, with statistical analysis performed via Wilcoxon signed-rank tests and PERMANOVA. Results showed that Ascomycota was the dominant fungal phylum in both treatment groups, with Saccharomyces, Penicillium, Candida, and Debaryomyces as prevalent genera. No significant changes occurred at the phylum level after switching to brodalumab, though minor genome-level variations were observed. Beta diversity analysis highlighted inter-patient variability, with no significant correlation between fungal composition and clinical outcomes. Despite improved clinical scores, the fungal gut microbiota remained largely stable, suggesting that brodalumab does not significantly alter fungal communities in psoriasis patients. Further research is needed for a comprehensive understanding.

Clinical outcomes and supragingival microbiota analysis around dental implants and teeth in patients with a history of periodontitis: a preliminary study of 6 months follow-up.

To investigate the supragingival microbiome surrounding dental implants and neighbouring tooth in periodontitis history and periodontally healthy patients. Subjects with a history of periodontitis (test) and periodontally healthy subjects (control) received one of two types of dental implants with different surface characteristics: sandblasted acid-etched (SLA) or precision dimension laser-treated (PDL). Periodontal clinical measurements were collected at baseline (V1), 3 months after implant placement (V4), at zirconia crown placement (V6) and 3 months after zirconia crown placement (V8). Supragingival bacterial microbiota was studied using Illumina MiSeq sequencing. Supragingival microbial community on SLA implants in test group significantly differed to control group at V8 (p < 0.05). A longitudinal shift displaying microbial dysbiosis occurred on SLA implants (p < 0.05) and adjacent teeth (p < 0.05) among test patients from V6 to V8. On PDL implants and the adjacent tooth, no significant difference between test and control groups from V6 to V8 (p > 0.05). Co-occurrence network in test group of SLA implants and the adjacent tooth at V8 showed increased disease-associated bacteria and reduced health-associated bacteria. Health-associated bacteria were dominant in control group of SLA implants at V8. The surface characteristics and prosthetic components of dental implants may be important risk factors in patients with a history of periodontitis. Dysbiosis of supragingival microbiome may predispose dental implants to peri-implant diseases. Thus, a strict supportive periodontal care plan is imperative to prevent early onset of biological complications.

Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free

BackgroundDNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.ResultsWe show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~ 4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were ≤ 1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12–15 h of sequencing.ConclusionOur results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.

Geographic location shapes fungal communities associated with Epidendrum roots

Fungal biodiversity significantly influences ecosystem dynamics through various interactions with plants, ranging from pathogenic to mutually beneficial associations. This study explores the fungal diversity associated with an ornamental orchid genus Epidendrum that is widely propagated globally but native to northern South America. Root samples were collected from Epidendrum in diverse geographic locations: Brazil, Colombia, Germany, Spain and six South African provinces. Fungal biodiversity was catalogued from the genomic DNA extracted from these roots using fungal-specific primers and Illumina MiSeq sequencing. Bioinformatic and statistical analyses revealed significant fungal diversity in the roots, with distinct dominant orders in each geographic region. Among the South African samples, significant differences were found in alpha diversity indices and species richness. Even though samples originating from different provinces overlapped in the PCoA plot, PERMANOVA indicated a significant difference in the fungal biodiversity, which was further supported by PERMDISP. In the global dataset, alpha diversity indices were insignificant, but species richness was. In the PCoA plot, data points clustered by sampling sites, indicating substantial differences in fungal biodiversity between the samples. This was validated by PERMANOVA and PERMDISP analyses. Outcomes from the core fungal analyses showed Epidendrum retained a conserved set of fungal orders from its native habitat when it transitioned to exotic regions, while it also formed new associations with local fungal communities in these introduced regions. These findings highlight the role of both core and region-specific fungal communities in the ecological adaptability and success of this widely planted orchid genus.

Temporal variation in the oral microbiome and the prediction of early childhood caries in different ethnicities.

Globally, early childhood caries (ECC) is a significant public health concern, necessitating effective prediction and prevention strategies. This study aimed to explore variations in the oral microbiome of saliva from pre-school Han and Uyghur children during ECC development and establish a predictive model based on temporal oral microbiome changes. Saliva samples were collected from a single kindergarten every three months over six months. Forty-four pre-school children provided 132 samples, categorized into six groups: (1) HEF (healthy pre-school Han children), (2) HEO (Han children with caries), (3) HEP (Han children with progressive caries), (4) WEF (healthy pre-school Uyghur children), (5) WEO (Uyghur children with caries), and (6) WEP (Uyghur children with progressive caries). Illumina Miseq sequencing identified oral microbiome differences between groups and time points. The Random Forest (RF) algorithm established ECC prediction models. The T1HEO group exhibited significantly higher Chaol index, observed species index, PD whole tree index, and Shannon index than the T2HEO group (p < 0.01). Similarly, the T1WEO group had significantly higher Chaol index, observed species index, and PD whole tree index than the T2WEO group (p < 0.05). The AUROC value for the ECC prediction model based on temporal oral flora changes was 0.517 (95% CI: 0.275-0.759) for pre-school Han children and 0.896 (95% CI: 0.78-1.00) for pre-school Uyghur children. In the onset of caries in pre-school Han children, bacterial species richness and community diversity in saliva declined, paralleled by a decrease in bacterial species richness in pre-school Uyghur children's oral saliva. The ECC prediction model grounded on temporal oral microflora changes exhibited robust predictive power, particularly for pre-school Uyghur children, potentially leading to more effective ECC prevention measures.

Energy metabolism, immune function, and intestinal flora in rats with kidney-yin deficiency treated with raw or saltwater-processed Phellodendron chinense Schneid

ObjectiveTo clarify the specific mechanisms of action of raw Phellodendron chinense Schneid. (RPC) and saltwater-processed PC (SPC) in the treatment of rats with a kidney-yin deficiency pattern (KYDP). MethodsHealthy rats were administered hydrocortisone to establish a KYDP model. The rats were divided into seven groups: blank control, model, positive control (Liuwei Dihuang pills), high-dose RPC, low-dose RPC, high-dose SPC, and low-dose SPC. Enzyme-linked immunosorbent assay was used to measure the levels of cAMP, cGMP, TRH, TSH, T3, T4, IFN-γ, TNF-α, and testosterone in the serum and the levels of Na+-K+-ATPase and Ca2+-Mg2+-ATPase in the liver. TRH mRNA expression in the rat hypothalamus was measured using RT-PCR. THRα1+2 protein expression in the hypothalamus of rats was measured using Western blot. Immunohistochemistry was performed to determine the expression levels of FAS, FasL, and TSHR. Flow cytometry was used to determine CD4+ and CD8+ T lymphocyte levels. Illumina MiSeq sequencing technology was used to evaluate the diversity of intestinal flora in KYDP rats. ResultsThe cAMP/cGMP ratio was significantly higher in the model group than in the blank control group (P = .048). Compared with the model group, after administration, the levels of the above-mentioned serum and liver indexes decreased, except that of testosterone. The CD4+/CD8+ ratio also decreased. Compared with the RPC group, the levels of T3, IFN-γ, FAS, FasL, and TSHR in the SPC group decreased whereas that of testosterone increased. Additionally, immune function and intestinal flora diversity improved in the SPC group. SPC proved to be more effective in improving liver energy metabolism in KYDP rats than RPC. ConclusionSPC had a better therapeutic effect on KYDP than RPC. The underlying mechanism of action may be related to improvements in liver energy metabolism, immune function, and intestinal flora diversity.

Enhancing biofilm formation with powder carriers for efficient nitrogen and phosphorus removal

This study assesses the improvement in nitrogen and phosphorus removal from wastewater achieved through the integration of zeolite and attapulgite carrier materials into the activated sludge (AS) process. It was found that the addition of these materials significantly enhanced the processing performance of the reactor. Specifically, the use of zeolite and attapulgite powders increased sludge particle sizes to averages of 231.56 μm and 219.62 μm, respectively. This facilitated micro-granule formation, substantially improving the settling characteristics of the sludge and boosting the activity and proliferation of essential microbes. Illumina MiSeq sequencing demonstrated significant accumulations of DGAOs (Candidatus_Competibacter) and DPAOs (Candidatus_Accumulibacter). Furthermore, these carriers augmented the protein content in extracellular polymers, enhancing the hydrophobicity of the sludge and promoting aggregation. Comparative analysis based on the extended Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory indicated a preferential adhesion affinity of sludge for zeolite compared to attapulgite, attributed primarily to Lewis acid-base and electric double-layer interactions. These findings underscore zeolite's enhanced efficacy in biomass fixation and suggest significant potential for the technological advancement of wastewater treatment plants.

Analysis of wheat fungal community succession in traditional storage structures using Illumina MiSeq sequencing technology

The diversity of fungi in wheat with different deoxynivalenol (DON) content at various periods post-harvest and in the environment of storage were investigated. The changes in DON content were measured with ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS), and an amplicon sequence analysis of fungi was performed in traditional storage structures using high-throughput sequencing. The changes in temperature, humidity, and CO2 concentration were collected by sensors. In addition, we analyzed principal component analysis, species composition, species differences, and community differences of fungi. There was an obvious separation of the fungal communities under different storage conditions and times. Many fungal genera were gradually decreasing during storage and were eventually undetectable, and many fungal genera that were undetectable at first gradually increased during storage and even became dominant fungal genera. The competition between fungi was fierce. The competition between fungi were affected by the presence of DON. As the initial DON content increased, the contribution of inter-group differences became more obvious. The temperature, humidity, and CO2 concentration of wheat in the silo's environment changed with extended storage time. The content of DON decreased with extended storage time. We had investigated the changes in DON content and their correlation with the changes in fungal communities and environmental factors, which showed a high degree of correlation. This study offers theoretical justification for optimizing safe wheat grain in traditional storage conditions.

Guangxi sour bamboo shoots: A study on microbial diversity and flavor characteristics across regions

Sour bamboo shoots, traditional salt-free fermented vegetables widely consumed in Guangxi province, are valued for their regionally varied flavor profiles and microbial diversity. This study employed HPLC, HS-SPME–GC–MS, and Illumina MiSeq sequencing to explore both the flavor profiles and the underlying microbial communities of 55 sour bamboo shoots from diverse regions in Guangxi. Our findings reveal the Tropic of Cancer as a pivotal boundary influencing quality divergence. It is noteworthy that three organic acids (succinic acid, acetic acid, and oxalic acid), nine amino acids (alanine, glutamate, glycine, valine, methionine, leucine, isoleucine, phenylalanine, and proline), and three volatile compounds (2-methoxy-4-methylphenol, p-cresol, and acetic acid) were found to be present in higher concentrations in samples from the northern region, suggesting the influence of a distinct terroir effect. Spearman correlation analysis preliminarily linked Lactobacillus, Enhydrobacter, and Lactiplantibacillus to the biosynthesis of key metabolites like p-cresol and 2-methoxy-4-methylphenol, highlighting their significant role in flavor production, although the exact mechanisms require further investigation. This study contributes to our understanding of the regional characteristics of sour bamboo shoots and provides a foundation for future research on the influence of microbiota on flavor. The findings may inform the development of traditional fermented products with a consistent flavor profile across regions.

Clostridium butyricum Prevents Diarrhea Incidence in Weaned Piglets Induced by Escherichia coli K88 through Rectal Bacteria-Host Metabolic Cross-Talk.

This study aimed to evaluate the effects of Clostridium butyricum (C. butyricum) on the prevention of the diarrhea rates and growth performances of weaned piglets induced by Escherichia coli K88 (E. coli K88). Twenty-four weaned piglets (6.92 ± 0.11 kg) were randomly assigned to one of three treatment groups for a period of 21 days. Each group consisted of eight pigs, with each pig being housed in an individual pen. Group I received the control diet along with normal saline, Group II received the control diet along with E. coli K88, and Group III received the control diet supplemented with 5 × 108 CFU/kg of C. butyricum and E. coli K88. We examined alterations in rectal microbiota and metabolites, analyzed the incidence of diarrhea, and investigated the interactions between microbiota and metabolites through the application of Illumina MiSeq sequencing and liquid chromatography-mass spectrometry. The results showed that, from days 14 to 21, the diarrhea incidence in Group III decreased significantly by 83.29% compared to Group II (p < 0.05). Over the entire experimental duration, the average daily feed intake of Group III decreased significantly by 11.13% compared to Group I (p < 0.05), while the diarrhea incidence in Group III decreased by 71.46% compared to Group II (p < 0.05). The predominant microbial flora in the rectum consisted of Firmicutes (57.32%), Bacteroidetes (41.03%), and Proteobacteria (0.66%). Administering E. coli K88 orally can elevate the relative abundance of Megasphaera (p < 0.05). Conversely, the supplementation of C. butyricum in the diet reduced the relative abundance of Megasphaera (p < 0.05), while increasing the relative abundance of unclassified_f_Lachnospiraceae (p < 0.05). Rectal metabolomics analysis revealed that supplementing C. butyricum in the feed significantly altered the amino acids and fatty acids of the piglets infected with E. coli K88 (p < 0.05). The correlation analysis showed that the occurrence of diarrhea was inversely related to adipic acid (p < 0.05) and positively associated with (5-hydroxyindol-3-YL) acetic acid and L-aspartic acid (p < 0.05). Prevotella_1 exhibited a negative correlation with octadecanoic acid (p < 0.05). Prevotellaceae_UCG-005 showed a negative correlation with (5-hydroxyindol-3-YL) acetic acid (p < 0.05). The findings from this research study aid in probiotic development and the enhancement of healthy growth in weaned piglets.

The impact of altered dietary adenine concentrations on the gut microbiota in Drosophila.

The gut microbiota influences host metabolism and health, impacting diseases. Research into how diet affects gut microbiome dynamics in model organisms is crucial but underexplored. Herein, we examined how dietary adenine affects uric acid levels and the gut microbiota over five generations of Drosophila melanogaster. Wild-type W1118 flies consumed diets with various adenine concentrations (GC: 0%, GL: 0.05%, and GH: 0.10%), and their gut microbiota were assessed via Illumina MiSeq sequencing. Adenine intake significantly increased uric acid levels in the GH group > the GC group. Despite no significant differences in the alpha diversity indices, there were significant disparities in the gut microbiota health index (GMHI) and dysbiosis index (MDI) among the groups. Adenine concentrations significantly altered the diversity and composition of the gut microbiota. High adenine intake correlated with increased uric acid levels and microbial population shifts, notably affecting the abundances of Proteobacteria and Firmicutes. The gut microbiota phenotypes included mobile elements, gram-positive bacteria, biofilm-forming bacteria, and gram-negative bacteria. The significantly enriched KEGG pathways included ageing, carbohydrate metabolism, and the immune system. In conclusion, adenine intake increases uric acid levels, alters gut microbiota, and affects KEGG pathways in Drosophila across generations. This study highlights the impact of dietary adenine on uric acid levels and the gut microbiota, providing insights into intergenerational nutritional effects.

Extramatrical mycelial biomass is mediated by fine root mass and ectomycorrhizal fungal community composition across tree species

In many ecosystems, a large fraction of gross primary production is invested in mycorrhiza. Ectomycorrhizal (ECM) mycelium is involved in regulating soil carbon and nutrient cycling. However, little is known about how mycelial biomass, production and turnover differ depending on ECM fungal community composition and associated tree species. We quantified fine root biomass and length using soil cores, and mycelial traits (biomass, production, and turnover) using mesh-bags and ergosterol analysis, and identified ECM exploration types by Illumina MiSeq sequencing of four ECM-dominated tree species (Picea asperata, Larix gmelinii, Quercus aquifolioides and Betula albosinensis) in subalpine forest. The ECM fungal community composition separated between needle-leaved and broadleaved species, and between evergreen and deciduous species. The ratio of mycelial to fine root biomass was similar across the species regardless of genus-scale community composition and the relative abundance of exploration types. Compared to the other species, Q. aquifolioides displayed higher fine root biomass and mycelial biomass and production, dominated by contact-short exploration type. Mycelial turnover rate tended to be lowest in P. asperata, dominated by medium-long exploration type. Much higher production of mycelium and only slightly higher turnover rate in Q. aquifolioides suggests that its steady-state mycelial biomass would be higher than of the other species. Moreover, compared to the two deciduous species, with similar production but somewhat lower turnover rate, the standing crop of mycelium in P. asperata may stabilize at a higher value. Our findings, that exploration type may affect production and turnover, highlight the importance of characterizing ECM fungal communities by exploration types when estimating the contribution of mycelium biomass to forest carbon sink and storage.

Altered gut microbiota and systemic immunity in Chinese patients with schizophrenia comorbid with metabolic syndrome

BackgroundMetabolic syndrome (MetS) is highly prevalent in individuals with schizophrenia (SZ), leading to negative consequences like premature mortality. Gut dysbiosis, which refers to an imbalance of the microbiota, and chronic inflammation are associated with both SZ and MetS. However, the relationship between gut dysbiosis, host immunological dysfunction, and SZ comorbid with MetS (SZ-MetS) remains unclear. This study aims to explore alterations in gut microbiota and their correlation with immune dysfunction in SZ-MetS, offering new insights into its pathogenesis.Methods and resultsWe enrolled 114 Chinese patients with SZ-MetS and 111 age-matched healthy controls from Zhejiang, China, to investigate fecal microbiota using Illumina MiSeq sequencing targeting 16 S rRNA gene V3-V4 hypervariable regions. Host immune responses were assessed using the Bio-Plex Pro Human Cytokine 27-Plex Assay to examine cytokine profiles. In SZ-MetS, we observed decreased bacterial α-diversity and significant differences in β-diversity. LEfSe analysis identified enriched acetate-producing genera (Megamonas and Lactobacillus), and decreased butyrate-producing bacteria (Subdoligranulum, and Faecalibacterium) in SZ-MetS. These altered genera correlated with body mass index, the severity of symptoms (as measured by the Scale for Assessment of Positive Symptoms and Scale for Assessment of Negative Symptoms), and triglyceride levels. Altered bacterial metabolic pathways related to lipopolysaccharide biosynthesis, lipid metabolism, and various amino acid metabolism were also found. Additionally, SZ-MetS exhibited immunological dysfunction with increased pro-inflammatory cytokines, which correlated with the differential genera.ConclusionThese findings suggested that gut microbiota dysbiosis and immune dysfunction play a vital role in SZ-MetS development, highlighting potential therapeutic approaches targeting the gut microbiota. While these therapies show promise, further mechanistic studies are needed to fully understand their efficacy and safety before clinical implementation.

Response of Soil Fungal Community to Reforestation on Shifting Sand Dune in the Horqin Sandy Land, Northeast China.

Reforestation of native shrub on shifting sand dunes has been widely used for desertification control in semi-arid grassland in Northeast China. Previous studies have confirmed that plantation establishment facilitates fixing sand dunes, restoring vegetation, and improving soil properties, but very few have focused on the response of the soil fungal community. In this study, a chronosequence of Caragana microphylla (CM) shrub sand-fixation plantations (8-, 19-, and 33-year-old), non-vegetated shifting sand dunes (0 years), and adjacent natural CM forests (NCFs; 50-year-old) in the Horqin sandy land were selected as experimental sites. Soil properties including enzymatic activities were determined, and the composition and structure of the soil fungal community were investigated using the Illumina MiSeq sequencing technique based on the internal transcribed spacer (ITS) rDNA. This study aimed to (1) describe the response of the soil fungal community to revegetation onto a moving sand dune by planting a native shrub plantation; (2) determine the main soil factors driving the succession of the fungal community; and (3) discuss whether the soil fungal community can be restored to its original state by reforestation. The reforestation of CM significantly ameliorated soil properties, increased soil fungal diversity, and altered the composition and structure of the soil fungal community. Ascomycota, Basidiomycota, and Zoopagomycota were the dominant phyla in all sites. Ascomycota did not respond to plantation development, whereas the other two dominant phyla linearly increased or decreased with the plantation age. The relative abundance of dominant genera varied with sites and showed a waning and waxing characteristic. The composition and structure of the soil fungal community in the 33-year CM plantation were very close to that of the NCF, indicating the restorability of the soil fungal community. The succession of the soil fungal community was directly driven by soil properties, of which soil moisture, organic matter, total N, urease, and protease were the main affecting factors.