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1.
Ying Yong Sheng Tai Xue Bao ; 33(4): 1118-1124, 2022 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-35543067

RESUMO

To reveal the formation mechanism of fungal community and diversity during the production of Shaoxing Huangjiu, we examined fungal communities in the samples of Linfanjiumu, Maiqu and fermentation mash based on Illumina MiSeq PE300 high-throughput sequencing platform. A total of 136000, 215283, 166150, and 143624 sequences were obtained from the samples of Linfanjiumu, Maiqu, initial mash and mature mash, respectively. After clustering, 32, 133, 107 and 84 OUT (operational taxonomic units) were obtained, respectively. The diversity and richness of fungi were in order of Maiqu > initial mash > mature mash > Linfanjiumu. At the level of phylum, Ascomycota were dominant in all samples. At genus level, Saccharomyces was dominant in Linfanjiumu, Aspergillus was dominant in Maiqu, and Saccharomyces and Aspergillus were the dominant fungi in the initial and mature mash. With the extension of the fermentation time, the proportion of Saccharomyces gradually increased in the mash, while other fungal groups including Aspergillus showed a decreasing trend. According to the results of PCoA analysis and similarity cluster analysis, the structure of fungi community in Linfanjiumu, initial mash and mature mash was much similar, while the fungal resources in Maiqu were quite different from other samples. The analysis of fungal community characteristics in the initial mash showed that the Linfanjiumu and Maiqu affected fungal diversity in Shaoxing Huangjiu. The dominant species of saccharification and fermentation starter (Linfanjiumu and Maiqu) played a leading role in driving community assembly of fermentation fungi.


Assuntos
Ascomicetos , Micobioma , Fermentação , Fungos/genética , Sequenciamento de Nucleotídeos em Larga Escala
2.
Arch Microbiol ; 204(6): 314, 2022 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-35545729

RESUMO

The gut mycobiome exhibits major influence on the gastrointestinal health and disease but received less attention due to low abundance. This study characterizes the fungal community and compares the microbial diversity between indoor and outdoor cats. Genomic DNA was extracted and sequenced by targeting the Internal Transcribed Spacer 1 (ITS1) region using Flongle flow cell on MinION™ sequencing platform. Results show the phylum Ascomycota and genus Peniophorella were numerous in indoor cats, whereas the Basidiomycota and Pichia were abundant in outdoor cats. Peniophorella formed the core mycobiome in both feline populations. Furthermore, alpha (p value = 0.0207) and beta diversities (p value = 0.009) results showed significant differences between the two groups. Overall, indoor cats have greater amounts of Peniophorella, whereas outdoor cats have higher Trichosporon and unclassified Sordariaceae. The study also suggests that keeping a cat indoors or left as a stray will affect their respective gut mycobiome.


Assuntos
Ascomicetos , Basidiomycota , Micobioma , Nanoporos , Animais , Ascomicetos/genética , Gatos , Fungos/genética
3.
Plant Signal Behav ; 17(1): 2068834, 2022 12 31.
Artigo em Inglês | MEDLINE | ID: mdl-35531979

RESUMO

Scutellaria baicalensis (SB), a traditional Chinese medicinal plant, is widely used because of its important pharmacological activities. However, the endophytic fungi that promote flavonoid accumulation in SB remain unclear. Therefore, we analyzed the endophytic fungal community of SB and screened the endophytic fungi that might promote flavonoid synthesis in SB. ITS1/ITS4Blast was used to identify the endophytic fungi in SB. In total, 687 strains were identified in 57 genera. The dominant genus in the leaves and stems was Alternaria and that in the roots was Fusarium. Alternaria was the dominant genus in SB collected from all sites and in wild and cultivated SB. Alpha diversity indexes indicated more abundant endophytic fungi in samples from Chengde, the genuine producing area of SB, than in those from other sites. Beta diversity index analysis indicated that SB plants with closer geographical relationships showed more similar endophytic fungal community profiles. Spearman correlation analysis revealed that baicalin, wogonoside, wogonin, and oroxylin A contents were significantly correlated with the relative abundance of Alternaria. Overall, the results indicate the importance of geographical factors in influencing the endophytic fungal community of SB and suggest that the presence of Alternaria spp. might contribute to flavonoid synthesis in SB.


Assuntos
Micobioma , Scutellaria baicalensis , Alternaria , Endófitos , Flavonoides , Fungos , Raízes de Plantas/microbiologia
4.
Front Cell Infect Microbiol ; 12: 848650, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35521219

RESUMO

Clinical and experimental studies indicate that the bacterial and fungal gut microbiota modulates immune responses in distant organs including the lungs. Immune dysregulation is associated with severe SARS-CoV-2 infection, and several groups have observed gut bacterial dysbiosis in SARS-CoV-2 infected patients, while the fungal gut microbiota remains poorly defined in these patients. We analyzed the fungal gut microbiome from rectal swabs taken prior to anti-infective treatment in 30 SARS-CoV-2 positive (21 non-severe COVID-19 and 9 developing severe/critical COVID-19 patients) and 23 SARS-CoV-2 negative patients by ITS2-sequencing. Pronounced but distinct interconnected fungal communities distinguished SARS-CoV-2 positive and negative patients. Fungal gut microbiota in severe/critical COVID-19 illness was characterized by a reduced diversity, richness and evenness and by an increase of the relative abundance of the Ascomycota phylum compared with non-severe COVID-19 illness. A dominance of a single fungal species with a relative abundance of >75% was a frequent feature in severe/critical COVID-19. The dominating fungal species were highly variable between patients even within the groups. Several fungal taxa were depleted in patients with severe/critical COVID-19.The distinct compositional changes of the fungal gut microbiome in SARS-CoV-2 infection, especially in severe COVID-19 illness, illuminate the necessity of a broader approach to investigate whether the differences in the fungal gut microbiome are consequences of SARS-CoV-2 infection or a predisposing factor for critical illness.


Assuntos
Ascomicetos , COVID-19 , Microbioma Gastrointestinal , Micobioma , Bactérias , Disbiose , Humanos , SARS-CoV-2
5.
Arch Microbiol ; 204(6): 302, 2022 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-35524014

RESUMO

Our aim was to explore the microbial community composition (bacteria and fungi) of fermented fish (pla-ra) from Northeast Thailand. We also made functional predictions concerning these microbial communities. The association between the microbiota and odor intensity was also analyzed. Fourteen samples of 1-year fermented fish samples derived from seven local markets in Khon Kaen, Northeast Thailand were used. The microbial community composition of each was investigated by sequencing the V1-V9 regions of the 16S rRNA gene (bacteria) and the ITS gene (fungi) using an Illumina MiSeq platform. Functional prediction analysis was conducted through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) based on the use of the bacterial 16S rRNA gene sequences. The bacterial communities were rich, comprising 402 genera from 28 phyla, including such genera as Tetragenococcus, Staphylococcus, Virgibacillus, Lactobacillus and Lentibacillus. The fungal communities comprised 7 phyla and 60 genera, such as Heterobasidion, Densospora, Exophiala and Monascus. The bacterial community functional analysis revealed an association with six biological metabolic pathway categories (e.g., metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems and human diseases) with 17 subfunctions, showing the richness of bacterial community functions. Odor-association analysis revealed that Brevibacterium, Brachybacterium and Chromohalobacter were more abundant in the weak-odor group, while Noviherbaspirillum was more abundant in the strong-odor group. This study provides a preliminary analysis of pla-ra microbial community structure and function in popular traditional Thai foods. Functional prediction analysis might be helpful to improve our knowledge of the microbiota in fermented fish.


Assuntos
Micobioma , Animais , Bactérias/genética , Fermentação , Peixes/microbiologia , Fungos/genética , Filogenia , RNA Ribossômico 16S/genética , Tailândia
6.
Zhongguo Zhong Yao Za Zhi ; 47(9): 2296-2303, 2022 May.
Artigo em Chinês | MEDLINE | ID: mdl-35531675

RESUMO

The continuous cropping obstacle of Gastrodia elata is outstanding, but its mechanism is still unclear. In this study, microbial changes in soils after G. elata planting were investigated to explore the mechanism correlated with continuous cropping obstacle. The changes of species and abundance of fungi and bacteria in soils planted with G. elata after 1, 2, and 3 years were compared. The pathogenic fungi that might cause continuous cropping diseases of G. elata were isolated. Finally, the prevention and control measures of soil-borne fungal diseases of G. elata were investigated with the rotation planting pattern of "G. elata-Phallus impudicus". The results showed that G. elata planting resulted in the decrease in bacterial and fungal community stability and the increase in harmful fungus species and abundance in soils. This change was most obvious in the second year after G. elata planting, and the soil microbial community structure could not return to the normal level even if it was left idle for another two years. After G. elata planting in soils, the most significant change was observed in Ilyonectria cyclaminicola. The richness of the Ilyonectria fungus in soils was significantly positively correlated with the incidence of G. elata diseases. When I. cyclaminicola was inoculated in the sterile soil, the rot rate of G. elata was also significantly increased. After planting one crop of G. elata and one to three crops of P. impudicus, the fungus community structure in soils gradually recovered, and the abundance of I. cyclaminicola decreased year by year. Furthermore, the disease rate of G. elata decreased. The results showed that the cultivation of G. elata made the Ilyonectria fungi the dominant flora in soils, and I. cyclaminicola served as the main pathogen of continuous cropping diseases of G. elata, which could be reduced by rotation planting with P. impudicus.


Assuntos
Gastrodia , Micobioma , Bactérias , Fungos , Gastrodia/microbiologia , Solo , Microbiologia do Solo
7.
NPJ Biofilms Microbiomes ; 8(1): 31, 2022 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-35477734

RESUMO

Deterministic and stochastic forces both drive microbiota assembly in animals, yet their relative contribution remains elusive, especially in wild aquatic-insect-associated fungal communities. Here, we applied amplicon sequencing to survey the assembly mechanisms of the fungal community in 155 wild stonefly individuals involving 44 species of 20 genera within eight families collected from multiple locations in China. Analysis showed that fungal diversity and network complexity differed significantly among the eight stonefly families, and that the fungal communities in stoneflies exhibited a significant distance-decay pattern across large spatial scales. Both a structural equation model and variance partitioning analysis revealed that environmental factors (e.g., geographical, climatic) outweigh host attributes in shaping the fungal community of stoneflies. Using neutral and null model analyses, we also find that deterministic processes play a larger role than stochasticity in driving the fungal community assembly. However, the relative contribution of ecological processes including dispersal, drift, and selection, varied strongly with host taxonomy. Furthermore, environmental conditions also significantly affect the strength of these ecological processes. Overall, our findings illustrate that variations in host attributes and environment factors may moderate the relative influence of deterministic and stochastic processes to fungal community composition in wild stoneflies, which provides new insights into mechanisms of microbial community assembly in aquatic arthropods.


Assuntos
Microbiota , Micobioma , Animais , China , Humanos , Insetos , Processos Estocásticos
8.
Arch Microbiol ; 204(5): 255, 2022 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-35412096

RESUMO

The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.


Assuntos
Metais Pesados , Micobioma , Poluentes do Solo , Biodegradação Ambiental , Metagenômica , Metais Pesados/metabolismo , Solo , Microbiologia do Solo , Poluentes do Solo/metabolismo
9.
mBio ; 13(2): e0244421, 2022 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-35404122

RESUMO

The kingdom Fungi is highly diverse in morphology and ecosystem function. Yet fungi are challenging to characterize as they can be difficult to culture and morphologically indistinct. Overall, their description and analysis lag far behind other microbes such as bacteria. Classification of species via high-throughput sequencing is increasingly becoming the norm for pathogen detection, microbiome studies, and environmental monitoring. With the rapid development of sequencing technologies, however, standardized procedures for taxonomic assignment of long sequence reads have not yet been well established. Focusing on nanopore sequencing technology, we compared classification and community composition analysis pipelines using shotgun and amplicon sequencing data generated from mock communities comprising 43 fungal species. We show that regardless of the sequencing methodology used, the highest accuracy of species identification was achieved by sequence alignment against a fungal-specific database. During the assessment of classification algorithms, we found that applying cutoffs to the query coverage of each read or contig significantly improved the classification accuracy and community composition analysis without major data loss. We also generated draft genome assemblies for three fungal species from nanopore data which were absent from genome databases. Our study improves sequence-based classification and estimation of relative sequence abundance using real fungal community data and provides a practical guide for the design of metagenomics analyses focusing on fungi. IMPORTANCE Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.


Assuntos
Microbiota , Micobioma , Bactérias/genética , Fungos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Microbiota/genética
10.
Front Immunol ; 13: 791152, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35401547

RESUMO

Multiple probiotics have protective effects against different types of liver injury. Different intestinal microbes could be beneficial to the protective effects of the probiotics on the treated cohorts in different aspects. The current study was designed to determine the intestinal bacterial and fungal microbiome associated with different cytokine profiles in the Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10 pretreated rats with D-galactosamine-induced liver injury. In this study, partition around medoids clustering analysis determined two distinct cytokine profiles (i.e., CP1 and CP2) comprising the same 11 cytokines but with different levels among the LI09, LI10, positive control (PC), and negative control (NC) cohorts. All rats in PC and NC cohorts were determined with CP1 and CP2, respectively, while the rats with CP1 in LI09 and LI10 cohorts had more severe liver injury than those with CP2, suggesting that CP2 represented better immune status and was the "better cytokine profile" in this study. PERMANOVA analyses showed that the compositions of both bacterial and fungal microbiome were different in the LI10 cohorts with different cytokine profiles, while the same compositions were similar between LI09 cohorts with different cytokine profiles. The phylotype abundances of both bacteria and fungi were different in the rats with different cytokine profiles in LI09 or LI10 cohorts according to similarity percentage (SIMPER) analyses results. At the composition level, multiple microbes were associated with different cytokine profiles in LI09 or LI10 cohorts, among which Flavonifractor and Penicillium were the bacterium and fungus most associated with LI09 cohort with CP2, while Parabacteroides and Aspergillus were the bacterium and fungus most associated with LI10 cohort with CP2. These microbes were determined to influence the cytokine profiles of the corresponding cohorts. At the structure level, Corynebacterium and Cephalotrichiella were determined as the two most powerful gatekeepers in the microbiome networks of LI09 cohort CP2, while Pseudoflavonifractor was the most powerful gatekeeper in LI10 cohort with CP2. These identified intestinal microbes were likely to be beneficial to the effect of probiotic Bifidobacterium on the immunity improvement of the treated cohorts, and they could be potential microbial biomarkers assisting with the evaluation of immune status of probiotics-treated cohorts.


Assuntos
Doença Hepática Crônica Induzida por Substâncias e Drogas , Microbioma Gastrointestinal , Micobioma , Animais , Bactérias , Bifidobacterium , Citocinas/farmacologia , Galactosamina/efeitos adversos , Humanos , Ratos
11.
PLoS One ; 17(4): e0266619, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35390087

RESUMO

This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.


Assuntos
Gengibre , Micobioma , Fungos/genética , Solo , Microbiologia do Solo , Água
12.
J Agric Food Chem ; 70(17): 5299-5309, 2022 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-35452238

RESUMO

Application of nitrification inhibitors (NIs) has been widely used to inhibit nitrification and reduce N2O emissions. However, the impacts of NI addition on soil carbon transformation and carbon-degrading microbial communities have not been well explored. Here, a microcosm experiment was carried out, and four treatments were designed: (i) unfertilized control, (ii) urea alone, (iii) urea plus cattle manure, and (iv) urea plus cattle manure with nitrapyrin. The influence of nitrapyrin on soil CO2 emissions, carbon-degrading extracellular enzyme activities, and the abundance and diversity of the cbhI community was investigated. Compared to the treatment of urea plus cattle manure, nitrapyrin significantly decreased cumulative CO2 emissions by 51.8%. Moreover, cbhI community gene copies and their α-diversities (P < 0.05) were also significantly reduced by nitrapyrin application. A partial least squares path model showed that CO2 emission was positively associated with cbhI community α-diversity but negatively associated with nitrapyrin addition. We conclude that the mitigation of soil CO2 emissions by nitrapyrin can be ascribed to its effects on decreasing of cellulose-degrading gene community diversity. Our findings provide new insights into the side-effects of nitrapyrin on abating CO2 emission.


Assuntos
Micobioma , Solo , Agricultura , Animais , Carbono , Dióxido de Carbono , Bovinos , Fertilizantes/análise , Esterco , Óxido Nitroso , Picolinas , Ureia
13.
Front Cell Infect Microbiol ; 12: 801331, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35425717

RESUMO

The effects of hydrogen sulfide (H2S) on diabetic metabolic disorders are still controversial, and the mechanisms underlying these effects remain largely unknown. This study was conducted to investigate the potential relationship between the gut microbiota and the improvement of diabetic metabolic disorders by exogenous H2S in obese db/db mice. The db/db mice were treated with sodium hydrosulfide (NaHS) (80 µmol/kg), or vehicle for 16 weeks, respectively. We measured the serum H2S, obesity parameters, glucose homeostasis, and triglyceride. The sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) in the cecal contents of NaHS-treated mice was performed to evaluate the gut microbial communities. We found that supplying exogenous H2S for 16 weeks significantly inhibited the increase of serum triglyceride, blood glucose, and insulin levels and altered specifically the gut bacterial microbiota structure in db/db mice. The relative abundance of some bacterial genera was correlated with the H2S or blood glucose level. Indeed, exogenous H2S increased Firmicutes and decreased Bacteroidetes at the phylum level along with changes of abundance of multifarious genera. Among them, Unclassified_Enterobacteriaceae, Prevotella, and Lactobacillus decreased and Unclassified_Ruminococcaceae, Oscillospira, Ruminococcus, Sutterella, and Desulfovibrio increased. For fungi, exogenous H2S decreased the abundance of Candida and Aspergillus. Here we demonstrated that, in diabetes, microbial dysbiosis may not be just limited to bacteria due to the inter-linked metabolic interactions among bacteria and fungi in the gut. The beneficial effects of exogenous H2S on diabetic metabolic disorders are likely associated with the alterations of specific microbiota.


Assuntos
Diabetes Mellitus Tipo 2 , Microbioma Gastrointestinal , Sulfeto de Hidrogênio , Doenças Metabólicas , Micobioma , Animais , Bactérias/genética , Glicemia , Diabetes Mellitus Tipo 2/complicações , Doenças Metabólicas/complicações , Camundongos , Camundongos Endogâmicos , Obesidade/complicações , RNA Ribossômico 16S/genética , Triglicerídeos
14.
PLoS One ; 17(4): e0267080, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35439275

RESUMO

The current study compared the gut mycobiomes of diabetic rats generated by a streptozotocin chemical challenge, diabetic rats with retinal changes and normal control rats over a period of 4 months. Sustained increase in blood sugar levels (>150 mg/dL) confirmed the induction of diabetes. Histology and immunohistochemistry were used to identify changes in the retinal tissues in the diabetic rats indicative of the animals progressing into diabetic retinopathy. Gut mycobiomes generated using faecal DNA, indicated dysbiosis at the genus level in both diabetic (DM) and diabetic rats with retinal changes (DRC) when compared with the control rats. In Tables 3-6 the specific genera that were significantly increased/decreased in DM1 and DM2 and in DRC1 and DRC2 respectively compared to the respective controls CT1-CT4 rats are listed. Further, the mycobiomes of the DM and DRC rats separated into distinct clusters following heat-map analysis of the discriminating genera. In addition, ß-diversity analysis separated the mycobiomes of DM and DRC rats from that of the control rats, but the mycobiomes of diabetic rats and diabetic rats with retinal changes showed an overlap. Based on the inferred functions of the discriminating genera in the mycobiomes, we speculated that increase in pathogenic fungi might contribute to the inflammatory status both in diabetic rats and rats showing retinal changes.


Assuntos
Diabetes Mellitus Experimental , Retinopatia Diabética , Micobioma , Animais , Diabetes Mellitus Experimental/complicações , Disbiose/microbiologia , Fezes/microbiologia , Ratos
15.
Environ Pollut ; 305: 119310, 2022 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-35430312

RESUMO

Bacterial and fungal communities have been widely applied as bio-indicators for ecological evaluation of copper (Cu) mine pollution in river sediments. However, the response pattern of their abundant and rare sub-communities is still unknown, limiting the further development of biological diagnostics. Here, the alpha-diversity, community composition, environmental contribution and co-occurrence network of total, abundant and rare taxa for bacteria and fungi in the Jiaopingdu Cu Mine wastewater treatment plant (WWTP) were investigated through high-throughput sequencing. The results revealed different responses of microbial alpha-diversity for abundant and rare sub-communities. The abundant taxa were ubiquitous in all sediments, while rare taxa exhibited increases of species richness in polluted areas because of heterochthonous inputs of WWTP drainage. Nevertheless, the variations of community composition were consistent for bacterial and fungal abundant and rare taxa, all of which showed significant dissimilarity between control and polluted areas. Distance-decay relationship and canonical correlation analysis indicated that abundant taxa assemblies (rbacteria = -0.924, rfungi = -0.684) were more strongly driven by environmental changes than rare ones (rbacteria = -0.626, rfungi = -0.349), because abundant microbes had higher proportions of significant variations in abundance. Co-occurrence networks revealed more keystone species with high node degree and centrality among abundant taxa compared with rare ones. Moreover, bacterial abundant and rare taxa were more sensitive to Cu mine pollution than relevant fungal taxa owing to different Cu tolerance. In conclusion, among all microbial sub-communities, abundant bacteria had the highest environmental sensitivity, suggesting their important application in biological diagnosis of Cu mine pollution. Accordingly, the abundant taxa could act as "key reservoir" for future selection of specific indicator species, for example Thiobacillus, while rare taxa no longer need excessive in-depth analysis, which would greatly improve microbial diagnosis efficiency.


Assuntos
Microbiota , Micobioma , Bactérias , Cobre/toxicidade , Rios
16.
Bioresour Technol ; 354: 127216, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35472639

RESUMO

Humus is the final product of humus precursors (HPS) during the humification process, while the associated mechanisms of humus formation have not been clarified. Here, the HPS degradation intermediate and core fungal function for wheat straw and chicken manure compost (SCM), cow dung compost (CD), Chinese traditional medicine residue compost (CTM) and mushroom dreg and chicken manure compost (MCM) was investigated during the thermophilic phase. The results showed SCM and MCM were rich in proteins, lipids, cellulose, low-molecular-weight organic acids, while CD and CTM contained abundant carbohydrates, aliphatic compounds, easily biodegradable aromatic structures, and intermediates from the lignocellulose degradation. In particular, the HPS degrading intermediates including O-alkyl-C and aromatic C compounds were the critical factors, and Scedosporium, Hypsizygus and Remersonia were the core fungal genera for the humification. Furthermore, the potential fungal functional genes involved in carbohydrate and lignin degradation might be the key factors to drive the humification process.


Assuntos
Agaricales , Compostagem , Micobioma , Animais , Bovinos , Feminino , Esterco , Solo
17.
FEMS Microbiol Ecol ; 98(5)2022 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-35404430

RESUMO

Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9 and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found that these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that either taxa dispersed to both terrestrial and aquatic habitats, or microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.


Assuntos
Microbiota , Micobioma , Archaea/genética , Bactérias/genética , Ecossistema , Salinidade , Madeira
18.
PLoS One ; 17(4): e0264556, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35472144

RESUMO

Trillions of microbes such as bacteria, fungi, and viruses exist in the healthy human gut microbiome. Although gut bacterial dysbiosis has been extensively studied in multiple sclerosis (MS), the significance of the fungal microbiome (mycobiome) is an understudied and neglected part of the intestinal microbiome in MS. The aim of this study was to characterize the gut mycobiome of patients with relapsing-remitting multiple sclerosis (RRMS), compare it to healthy controls, and examine its association with changes in the bacterial microbiome. We characterized and compared the mycobiome of 20 RRMS patients and 33 healthy controls (HC) using Internal Transcribed Spacer 2 (ITS2) and compared mycobiome interactions with the bacterial microbiome using 16S rRNA sequencing. Our results demonstrate an altered mycobiome in RRMS patients compared with HC. RRMS patients showed an increased abundance of Basidiomycota and decreased Ascomycota at the phylum level with an increased abundance of Candida and Epicoccum genera along with a decreased abundance of Saccharomyces compared to HC. We also observed an increased ITS2/16S ratio, altered fungal and bacterial associations, and altered fungal functional profiles in MS patients compared to HC. This study demonstrates that RRMS patients had a distinct mycobiome with associated changes in the bacterial microbiome compared to HC. There is an increased fungal to bacterial ratio as well as more diverse fungal-bacterial interactions in RRMS patients compared to HC. Our study is the first step towards future studies in delineating the mechanisms through which the fungal microbiome can influence MS disease.


Assuntos
Ascomicetos , Esclerose Múltipla , Micobioma , Ascomicetos/genética , Bactérias/genética , Disbiose/microbiologia , Fungos/genética , Humanos , Micobioma/genética , RNA Ribossômico 16S/genética
19.
Cells ; 11(8)2022 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-35455967

RESUMO

Bacteria, as well as eukaryotes, principally fungi, of the upper respiratory tract play key roles in the etiopathogenesis of respiratory diseases, whereas the potential role of archaea remains poorly understood. In this review, we discuss the contribution of all three domains of cellular life to human naso- and oropharyngeal microbiomes, i.e., bacterial microbiota, eukaryotes (mostly fungi), as well as the archaeome and their relation to respiratory and atopic disorders in infancy and adolescence. With this review, we aim to summarize state-of-the-art contributions to the field published in the last decade. In particular, we intend to build bridges between basic and clinical science.


Assuntos
Asma , Microbiota , Micobioma , Archaea , Bactérias , Criança , Eucariotos , Fungos , Humanos
20.
Int J Food Microbiol ; 372: 109678, 2022 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-35447529

RESUMO

Multi-mycotoxin contamination of barley reduces malt quality and also poses serious health risks to both humans and animals. Among the detected mycotoxins in barley, Fusarium and Alternaria toxins represent severe food safety issues due to their widespread prevalence and strong synergistic toxicity. In this study, the effects of Fusarium and Alternaria fungi and their related toxins were investigated using simulated malting process conditions for contaminated barley samples. The dynamic changes of the fungal community and their associated mycotoxins were analyzed via high-throughput sequencing and UHPLC-q-trap-MS/MS, respectively. The results showed significant differences in the fungal communities between barley grains and their associated malt samples. These differences were noted for the following: fungal community diversity, dominant flora and the fungal structures at phylum, genus, and family level. Additionally, significant changes in the levels of alternariol monomethyl ether, tentoxin, zearalenone, and 15Acetyl-Deoxynivelenone were observed (p < 0.05) during the malting process. These results provide valuable information for strategies aimed at controlling fungal infections and the presence of mycotoxins in malt, so as to ensure food safety and human health.


Assuntos
Fusarium , Hordeum , Micobioma , Micotoxinas , Alternaria/genética , Contaminação de Alimentos/análise , Fusarium/genética , Hordeum/microbiologia , Micotoxinas/análise , Plântula/química , Espectrometria de Massas em Tandem
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