Fungal Microbiome Research Articles

Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone.

Environmental impacts of the 1986 Chernobyl Nuclear Power Plant accident are much debated, but the effects of radiation on host microbiomes have received little attention to date. We present the first analysis of small mammal gut microbiomes from the Chernobyl Exclusion Zone in relation to total absorbed dose rate, including both caecum and faeces samples. We provide novel evidence that host species determines fungal community composition, and that associations between microbiome (both bacterial and fungal) communities and radiation exposure vary between host species. Using ambient versus total weighted absorbed dose rates in analyses produced different results, with the latter more robust for interpreting microbiome changes at the individual level. We found considerable variation between results for faecal and gut samples of bank voles, suggesting faecal samples are not an accurate indicator of gut composition. Associations between radiation exposure and microbiome composition of gut samples were not robust against geographical variation, although we identified families of bacteria (Lachnospiraceae and Muribaculaceae) and fungi (Steccherinaceae and Strophariaceae) in the guts of bank voles that may serve as biomarkers of radiation exposure. Further studies considering a range of small mammal species are needed to establish the robustness of these potential biomarkers.

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

The core gut microbiome of adult honeybee comprises a set of recurring bacterial phylotypes, accompanied by lineage-specific, variable, and less abundant environmental bacterial phylotypes. Several mutual interactions and functional services to the host, including the support provided for growth, hormonal signaling, and behavior, are attributed to the core and lineage-specific taxa. By contrast, the diversity and distribution of the minor environmental phylotypes and fungal members in the gut remain overlooked. In the present study, we hypothesized that the microbial components of forager honeybees (i.e., core bacteria, minor environmental phylotypes, and fungal members) are compartmentalized along the gut portions. The diversity and distribution of such three microbial components were investigated in the context of the physico-chemical conditions of different gut compartments. We observed that changes in the distribution and abundance of microbial components in the gut are consistently compartment-specific for all the three microbial components, indicating that the ecological and physiological interactions among the host and microbiome vary with changing physico-chemical and metabolic conditions of the gut.

Above-ground parts of white grapevine Vitis vinifera cv. Furmint share core members of the fungal microbiome.

Grapevine (Vitis vinifera) is a reservoir of fungal endophytes that may affect its growth, health status and grape production. Although there is growing interest in comparing fungal communities of mainly red grape varieties across various factors using only high-throughput sequencing, the small-scale mycobiome variations in geographically close vineyards need further examination. We aimed to characterize the fungal microbiome of the above-ground tissues of V. vinifera cv. Furmint in different plant parts, seasons and sites using culture-dependent and culture-independent methods, and in planta fluorescent microscopic visualization techniques. Samples were collected from four sites of the Tokaj wine region in Mád and two reference sites in Eger, Hungary, across different seasons for 2 years. Fungal endophytes of young and mature leaves, flowers and grape bunches were collected at different phenological stages. Based on each technique, Aureobasidium pullulans, Cladosporium spp. and the complex species Alternaria alternata dominated the community at every site, season and plant organ. We found no significant difference among communities in distinct neighbouring vineyards, nor when compared with the distant reference sites. We can conclude that the different shoot parts of the Furmint grapevines harbour a common core group of fungal community in these regions.

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides

BackgroundMutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica.ResultsTo investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations.ConclusionsThe genomic characterization of five yeast strains isolated from N. vespilloides resulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation.

The gut microbiota in patients with COVID‐19 and obesity

The COVID‐19 pandemic is caused by the novel coronavirus SARS‐CoV‐2. Obesity is one of the major comorbidities that are related to complications in the course of the disease. Obesity is characterized by a chronic low grade of inflammation and it is proposed that abnormal gut microbiota together with increased gut permeability are risk factors of this pathology. The aim of the present study was to conduct a descriptive research and investigate about the imbalance in the gastrointestinal microbiota (dysbiosis) in patients with COVID‐19 and obesity. A library research using the electronic databases PubMed and Google Scholar was performed. The full search strategy combined terms from three themes: COVID‐19, obesity, and gut microbiota. Terms were searched as both keywords (title/abstract words) and a comprehensive list of MeSH terms related to each theme. Titles and abstracts were reviewed for relevance and then screened considering the full text content. Network maps were also generated to evaluate the co‐ocurrence terms in the papers analyzed using VOSviewer 1.6.14 software. Several studies indicate that gut microbiota is altered in COVID‐19 patients showing a decrease in abundance and diversity. Different opportunistic pathogens were found increased in COVID‐19 patients including Collinsella, Streptococcus, Morganella, Rothia, Veillonella, Erysipelatoclostridium, Actinomyces, Coprobacillus and Clostridium. Many of them were associated with an increased in SARS‐CoV‐2 infectivity, inflammatory markers, or COVID‐19 disease severity. Fecal fungal microbiome was also altered showing an enrichment of fungal pathogens from the genera Candida and Aspergillus. There is a correlation between the bacterial species present in the gut microbiota of COVID‐19 patients and in patients with obesity. This was observed principally in the increment of Firmicutes, Actinobacteria and Proteobacteria and the decrease of Bacteroidetes. Modulation of gut microbiota with prebiotics, probiotics and synbiotics are suggested to be used in patients with COVID‐19. The present study contributes to highlight the importance of gastrointestinal microflora in COVID‐19 patients with obesity as well as the necessity to study specifically this population which report a higher risk of COVID‐19 morbidity and mortality. Further studies are needed to evaluate potential treatments to reestablish gut microbiome, reduce inflammation, and improve immune function considering the persistence of SARS‐CoV‐2 in the gastrointestinal tract.

Fungal Microbiome; Mycobiome

Bakteriyel mikrobiyom analiz ve araştırmaları, mantar mikrobiyomu kavramı ve çalışmalarının önüne geçmiştir. Tüm insanlar ve laboratuvar hayvanları, sağlıklı olduklarında doğal mantar topluluklarını taşırlar. Mantar mikrobiyomu, bakteriyel mikrobiyomdan önemli ölçüde daha küçüktür. Hastalıkta kofaktör olarak mantar mikrobiyomunun rolü de belirgindir ancak bunca zamanda hafife alınmıştır. Sağlıklı bir derinin fungal mikrobiyomunda yer alan başlıca türler Malassezia ve Candida türleridir. Sağlıklı deride daha fazla maya formu görülürken, etkilenen bölgelerde daha çok hifal formda görülmektedir. Ağız mikrobiyomunun fungi içerdiği kabaca Candida, Aspergillus, Fusarium ve Cryptococcus sp den oluşmaktadır. Sağlıklı akciğerlerin steril olduğu savı da son yıllarda yapılan sekans çalışmaları ile değişmiş, fungal topluluklardan Aspergillus fumigatus başta olmak üzere Ceriporia lacerata, Saccharomyces cerevicae ve Penicillium brevicompactum’un bulunduğunu gösterilmiştir. İnflamatuar bağırsak hastalıklarında belirgin fungal mikrobiyal disbiyoz bulunmuş, Basidiomycota / Ascomycota oranı ve C. albicans’ın arttığı, Saccharomyces cerevisiae oranının ise azalmış olduğu belirlenmiştir. Sonuçta; Bu tür karmaşık ve birbirine bağlı mikrobiyal sistemlerde, mikobiyom, bir dizi hastalığa ve bunların patogenezine katkıda bulunan bir faktör olabilir. İleri çalışmalar kısa sürede bu tür konulara açılım getirecektir.

<p><strong><em>Pyrenochaetopsis kuksensis</em> (<em>Pyrenochaetopsidaceae</em>), a new species associated with an ornamental boxwood in the Czech Republic</strong></p>

During the investigation of fungal microbiome associated with boxwood in the Czech Republic, samples from Buxus sempervirens L. (Buxaceae) plants were collected and used for isolation. Two fungal strains were proposed as a new species Pyrenochaetopsis kuksensis based on morphology as well as phylogenetic analyses of ITS, LSU, rpb2, and tub2 sequence data. Detailed descriptions and phylogenetic relationships of the new taxon are provided.

Parasites, niche modification and the host microbiome: A field survey of multiple parasites.

Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.

Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo.

Recently, it was shown that long-term plant breeding does not only shape plant characteristics but also impacts plant-associated microbiota substantially. This requires a microbiome-integrative breeding approach, which was not yet shown. Here we investigate this for the Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) by analyzing the microbiome of six genotypes (the complete pedigree of a three-way cross-hybrid, consisting of three inbred lines and one open pollinating cultivar) in the seed and rhizosphere as well as the progeny seeds. Using high-throughput amplicon sequencing targeting the 16S rRNA and the ITS1 genes, the bacterial and fungal microbiomes were accessed. Seeds were found to generally carry a significantly lower microbial diversity compared to the rhizosphere and soil as well as a different microbial composition, with an especially high fraction of Enterobacteriaceae (40–83%). Additionally, potential plant-beneficial bacterial taxa, including Bacillaceae, Burkholderiaceae, and Pseudomonadaceae, were found to be enriched in progeny seeds. Between genotypes, more substantial changes can be observed for seed microbiomes compared to the rhizosphere. Moreover, rhizosphere communities were assembled for the most part from soil. Interestingly, bacterial signatures are mainly linked from seed to seed, while fungal communities are shaped by the soil and rhizosphere. Our findings provide a deep look into the rhizosphere and seed microbiome assembly of pumpkin-associated communities and represent the first steps into microbiome-driven breeding for plant-beneficial microbes.

Seasonal Variations in the Gut Fungal Communities of Hooded Crane (Grus monacha) at Wintering and Stopover Sites in China.

Simple SummaryThe gut fungi assist the host in various physiological activities, homeostasis, immune responses, and growth. The diversity and community composition of gut fungi are driven by multiple factors, including diet, environmental exposure, habitat type, and seasonal migration. Migratory birds have a peculiar life cycle, so it is interesting to understand the ecological function of their “gut fungal microbiome.” Birds are exposed to variable diets, environments, and habitats amid seasonal migration. The hooded crane is known as a long-distance migratory bird, inhabiting both wintering and stopover grounds during seasonal migration. During migratory seasons, it inhabits various habitats and is exposed to variable environments. This study analyzed the shifts between gut fungal diversity and the community composition of the hooded crane at both wintering and stopover sites amid seasonal migration. The gut fungal alpha diversity exhibited a more significant change during winter than in fall and spring. The gut fungal community composition exhibited significant shifts across winter, fall, and spring (ANOSIM, p = 0.001). The pathogenic diversity and relative abundance showed significant differences during winter at the wintering site relative to fall and spring at the stopover site. Moreover, the pathogenic fungal community composition was significantly different during fall, winter, and spring. This work contributes to present essential knowledge about the gut fungal microbiome of hooded cranes amid seasonal migration. This study also implicated that conservation measures for hooded crane conservation should be applied, as the risk of cross-transmission of potential fungal pathogens might increase during seasonal migration.The “gut fungal microbiome” maintains the immune system, homeostasis, and various physiological functions of an organism. Different factors shape and affect gut fungal diversity and community composition, such as environment, habitat type, food resources, and seasons during migration. Wild birds amid migration are exposed to different habitats with different environments, available food resources, and seasons, which may substantially impact their gut fungal community composition and diversity. The hooded crane (Grus monacha) is a known migratory bird that migrates over long distances and is exposed to varied habitats with different environments and food types. We investigated the differences in gut fungal diversity and community composition between wintering and stopover sites amid three migratory seasons. We deduced the gut fungal pathogenic diversity and community composition during winter, fall, and spring by using high throughput sequencing (Illumina Mi-seq), and the internal transcribed region 2 (ITS2) was examined. Samples were collected from Shengjin Lake in the winter and Lindian during the fall and spring. The dominant fungal phyla found across the three seasons were Ascomycota, Basidiomycota, Zygomycota, and Rozellomycota. The gut fungal alpha diversity showed significant shifts during winter at the wintering site compared with the fall and spring seasons at the stopover site. The fungal community composition exhibited a significant change across the three seasons (ANOSIM p = 0.001). The results also demonstrated that the diversity and relative abundance of potential pathogens also showed divergence in winter compared to fall and spring. This study provides the basis for understanding the discrepancy in gut fungal diversity and community composition during migratory seasons at both wintering and stopover grounds. It also suggests that conservation measures should be applied to the conservation of hooded cranes and other wild birds, as the risk of cross-infection increases during seasonal migration.

Assessment of bacterial and fungal populations in urine from clinically healthy dogs using next-generation sequencing.

BackgroundUrine from clinically healthy dogs is not sterile. Characterizing microbial diversity and abundance within this population of dogs is important to define normal reference ranges for healthy urine.ObjectivesTo establish composition and relative representation of bacterial and fungal microbiomes in urine of clinically healthy dogs.AnimalsFifty clinically healthy dogs.MethodsAnalytic study. Urine sampling via cystocentesis. Comprehensive evaluation of urine including standard urinalysis, culture and sensitivity, next‐generation sequencing (NGS), and bioinformatics to define bacterial and fungal microbiome.ResultsCulture did not yield positive results in any samples. Next‐generation sequencing of urine established low presence of bacteria, fungi, or both in all samples. Diversity and abundance of bacterial and fungal communities varied between urine samples from different dogs. Struvite crystals were associated with bacterial community structure (P = .07) and there was a positive correlation between struvite crystals and pH.Conclusions and Clinical ImportanceThe microbiome in urine of clinically healthy dogs has diverse bacterial and fungal species These findings highlight limitations of conventional culture testing and the need for culture‐independent molecular diagnostics to detect microorganisms in urine.

Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain).

We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.

A roadmap from unknowns to knowns: Advancing our understanding of the microbiomes of commercially available tobacco products.

Tobacco smoking is still the leading cause of preventable diseases and death in the USA and throughout the globe. Under Section 904(a)(3) of the US Federal Food, Drug, and Cosmetic Act, tobacco manufacturing companies need to report on quantities of harmful and potentially harmful constituents (HPHCs) in all tobacco products. While the extensive HPHC list of 2012 includes 93 chemicals, which are categorized as carcinogenic, respiratory, cardiovascular, or reproductive toxicants or addictive compounds, it fails to include microorganisms (bacteria and fungi) that have been shown to contribute to adverse health outcomes among tobacco users. Nevertheless, over the last 50 years, researchers have studied microorganisms in a variety of tobacco products using both culture-based and culture-independent techniques. In this mini-review, we provide an overview of this body of research, detailing the bacterial and fungal microbiomes residing in commercial tobacco products. Overall, studies have characterized over 89 unique bacterial genera and 19 fungal genera in cigarettes, cigars, cigarillos, hookah, and smokeless tobacco. The most predominant bacterial genera are Bacillus, Pseudomonas, and Staphylococcus. Fungal genera identified have included Aspergillus, Penicillium, Mucor, Alternaria, Cladosporium, Streptomyces, and Candida, to name a few. While some of the identified microorganisms are known human pathogens, others are potential opportunistic pathogens. Given the vast array of microorganisms that are present across diverse types of tobacco products, future research should be focused on the viability of these microorganisms, as well as their ability to transfer to the user’s respiratory tract, potentially contributing to adverse health outcomes.Key points• Commercial tobacco products harbor diverse bacterial and fungal communities.• Some of these microorganisms are known or opportunistic human pathogens.• Research on their viability and transmission to users’ respiratory tracts is needed.

Mycobiome analysis for distinguishing the geographical origins of sesame seeds

Sesame (Sesamum indicum) is one of the most widely cultivated crops in Asia and Africa. The identification of the geographical origins of sesame seeds is important for the detection of fraudulent samples. This study was conducted to build a prediction model and suggest potential biomarkers for distinguishing the geographical origins of sesame seeds using mycobiome (fungal microbiome) analysis coupled with multivariate statistical analysis. Sesame seeds were collected from 25 cities in Korea, six cities in China, and five sites in other countries (Ethiopia, India, Nigeria, and Pakistan). According to the expression of fungal internal transcribed spacer (ITS) sequences in sesame seeds, 21 fungal genera were identified in sesame seeds from various countries. The optimal partial least squares-discriminant analysis model was established by applying two components with unit variance scaling. Based on seven-fold cross validation, the predictive model had 94.4% (Korea vs. China/other countries), 91.7% (China vs. Korea/other countries), and 88.9% (other countries vs. Korea/China) accuracy in determining the geographical origins of sesame seeds. Alternaria, Aspergillus, and Macrophomina were suggested as the potential fungal genera to differentiate the geographical origins of sesame seeds. This study demonstrated that mycobiome analysis could be used as a complementary method for distinguishing the geographical origins of raw sesame seeds.

Diversity and Spatiotemporal Distribution of Fungal Endophytes Associated with Salvia multicaulis.

Salvia multicaulis has been an important medicinal plant in Iran and several East Asian countries for hundreds of years. Because of growing demand, overharvesting of wild S. multicaulis has endangered its wild populations. Endophytes are well known for protecting wild plant populations against biotic and abiotic stresses, especially under harsh situations, as well as for their plant growth enhancement activities. Since no information was on endophyte biology in S. multicaulis, here we aimed at analyzing diversity and spatiotemporal distribution of fungal endophytes associating S. multicaulis in their main wild habitats in Iran, i.e., Qazvin, Alborz and Mazandaran provinces. A total of 153 fungal endophytes were isolated and identified according to their morphology and ribosomal ITS rDNA sequences. As results indicated Ascomycota dominated in colonizing S. multicaulis with a relative frequency (RF) of 96.77%, comprising of Eurotiomycetes (RF: 40.5%), Sordariomycetes (RF: 33.9%) and Dothideomycetes (RF: 20.5%). Mucoromycota, comprised the rest of endophytes (RF: 5.23%). The entire fungal microbiome was classified into nine genera including Fusarium (25.5%), Penicillium (21.5%), Aspergillus (17.0%), Alternaria (15.5%), Colletotrichum (5.2%), Rhizopus (5.2%), Macrophomina (4.5%), Trichoderma (3.25%) and Nodulisporium (2.0%). Analyses of different diversity indices indicated significant correlations with tissue type, sampling locations and season of recovery. Almost 43% of fungal endophytes were recovered at Mazandaran, Kojur; 35.4% at Qazvin, Barajin Forest Park; 30.1% at Alborz, Taleqan; and 21% at Alborz, Mahdasht. The highest overall endophyte recovery was in summer (36.8%), followed by spring (31.6%), autumn (21%), and winter (10.5%). In total, the number of endophytes recovered from roots (91) was higher than those of stems (32) and leaves (30), especially during autumn and winter. Accordingly, we conclude that Ascomycota are the major endophytic fungi colonizing S. multicaulis, and that sampling location, tissue type and season can affect the fungal endophyte composition of this medicinal plant. This knowledge could be further applied in protection and health management of this endangered species.

Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease

Little is known about airway mycobiome, and its relationship with bacterial microbiome in chronic obstructive pulmonary disease (COPD). Here we report the first simultaneous characterization of sputum bacterial and fungal microbiome in 84 stable COPD and 29 healthy subjects, using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing. Ascomycota predominated over Basidiomycota in fungal microbiome both in COPD patients and healthy controls. Meyerozyma, Candida, Aspergillus and Schizophyllum were most abundant at the genus level. There was a significant inverse correlation between bacterial and fungal microbial diversity, both of which altered in opposite directions in COPD patients versus controls, and in frequent versus non-frequent exacerbators. An enhanced bacterial-fungal ecological interaction was observed in COPD patients, which was characterized by higher proportion of co-occurrence intrakingdom interactions and co-exclusive interkingdom interactions. In COPD, four mutually co-occurring fungal operational taxonomic units (OTUs) in Candida palmioleophila, Aspergillus and Sordariomycetes exhibited co-exclusive relationships with other fungal OTUs, which was specifically present in frequent exacerbators but not in non-frequent exacerbators. The perturbed bacterial-fungal interactions in COPD were associated with increased airway inflammatory mediators such as IL-6 and IL-8. The disruption of airway bacterial-fungal community balance, characterized by the loss of commensal bacterial taxa and enriched pathogenic fungal taxa, is implicated in COPD. The emergence of pathogenic fungi such as Candida and Aspergillus could be a marker for the frequent exacerbator phenotype. The airway mycobiome is an important cofactor mediating pathogenic infection and host inflammation in COPD.

First assessment of the stool mycobiome in patients (pts) with metastatic renal cell carcinoma (mRCC) receiving targeted therapy (TT) or immunotherapy (IO).

337 Background: Previous studies have associated specific stool bacterial species with response to both targeted therapy and immunotherapy (Routy et al Science 2018; Dizman et al Cancer Med 2020). Abundant fungal elements also constitute the human microbiome (the so-called “mycobiome”); we explore whether these could be related to clinical benefit (CB) from TT. Methods: Pts from 2 simultaneously conducted studies were included in the analysis. Both studies enrolled patients with histologically confirmed RCC with metastatic disease; in one study, pts received standard of care (SOC) TT, while in the other pts received SOC IO. In both studies, stool was collected at baseline and at multiple timepoints thereafter. Whole metagenome sequencing was performed for fungal microbiome composition (TGen North, AZ). Linear discriminant analysis (LDA) effect size (LEfSe) was used for comparison of the gut mycobiome in patients who obtained clinical benefit (CB; complete response, partial response or stable disease > 6mos) versus no clinical benefit (NCB; progressive disease or stable disease ≤6mos) from TT or IO. Results: A total of 50 samples from 24 pts (19:5 M:F) were included in the analysis. The majority of pts (19; 79%) had clear cell histology. 15 pts received TT while 9 pts received IO. The fungal genera demonstrating the highest abundance was Saccharomyces with a median relative abundance of 86.9% (range, 11%-99%). LEfSe performed in different taxonomic levels revealed Malassezia globosa (LDA = 4.93; P = 0.038) and Alternaria infectoria (LDA 4.94; P = 0.018) as gut mycobiome components associated with NCB, and order Russulales associated with CB from TT (LDA = 4.93; P = 0.018). In contrast, no association was identified between mycobiome profile and CB in the IO-treated group. The presence of several pathogenic fungi such as Candida albicans and Aspergillus fumigatus was noted in a minority of pts and did not have any bearing on clinical outcome. In pts with serial samples, a trend towards decreasing Saccharomyces spp. (the most abundant species) and increasing fungal diversity was noted. Conclusions: Our study is the first to highlight potential associations between the mycobiome and CB with TT. Our finding of Malassezia spp resulting in lack of CB with TT bolsters findings from Aykut et al (Nature 2019), implicating the same genera in progression of pancreatic cancer. Confirmation of these findings in larger series is underway.

Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor.

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

Increasing aridity shapes beta diversity and the network dynamics of the belowground fungal microbiome associated with Opuntia ficus-indica

AimsThe effects of aridity on soil and water-use efficient (WUE) crop species are relatively well known. However, the understanding of its impacts on the dynamics of below-ground microorganisms associated with plant roots is less well understood. MethodsTo investigate the influence of increasing aridity on the dynamics of the fungal communities, samples from the root endosphere and rhizosphere associated with the prickly pear cactus trees (Opuntia ficus-indica) growing along the aridity gradient were collected and the internal transcribed spacer (ITS) were sequenced. The diversity and network analyses of fungal taxa were determined along with standard measurements of soil parameters. ResultsWe found that (i) the fungal community exhibited similar alpha diversity and shared a set of core taxa within the rhizosphere and endosphere, but there was significant beta diversity differences; (ii) the relative abundance of major phyla was higher in the rhizosphere than in the endosphere; (iii) arbuscular endomycorrhizal colonization was highest in the humid climate and decreased under lower-arid, and was negatively correlated with increased concentration of Ca2+ in the soil; (iv) increased aridity correlated with increased connectivity of the soil microbial-root fungal networks in the arid soils, producing a highly cohesive network in the upper-arid area; and (v) distinct fungal hubs sculpt the fungal microbiome network structure in the rhizosphere and endosphere within each bioclimatic zone. ConclusionsOur findings highlight the importance of gradient analysis-based correlation network as a powerful approach to understand changes in the diversity, the dynamics, and the structure of fungal communities associated with the rhizosphere-endosphere interaction and led to the identification of microbes at each bioclimatic zone that are potentially involved in promoting the survival, protection, and growth of Opuntia trees. The variability of fungal hubs composition depending on plant compartment and bioclimatic zone will give key implications for the application of rhizospheric fungi and endophytes as microbial inoculants in agriculture, as well as in the conservation and restoration of cacti plants in arid and semi-arid lands against the backdrop of climate change. Overall, this study will enhance our understanding of the microbiomes'dynamic of CAM plants in nature.

Dynamic characteristics and co-occurrence patterns of microbial community in tobacco leaves during the 24-month aging process

PurposeMicroorganisms are important in tobacco aging. These are used to improve the quality of tobacco leaves after threshing and redrying. However, the response of microbial community to the storage environment and time during the tobacco aging process has been less explored. This study aimed to characterize the dynamic changes in microbial community composition and diversity in tobacco leaf samples.MethodsIn this study, 16S and ITS rRNA gene amplicon sequencing techniques were used to characterize the composition, diversity, and co-occurrence of the microbial community in tobacco leaves stored in two different cities during the 24-month aging. Furthermore, the activities of several enzymes were measured spectrophotometrically, and the correlation between the microbiota and enzyme activity was analyzed by network analysis.ResultsShannon diversity and Chao richness of bacterial communities gradually increased during the first 18 months, whereas those of the fungal community decreased. The relative abundance of Proteobacteria decreased, whereas that of Actinobacteria and Bacteroidetes increased. The proportion of Ascomycota gradually increased during the first 18 months and then rapidly decreased, whereas the proportion of Basidiomycota exhibited a completely opposite pattern. The change in the composition of bacterial community and dominant genera in leaves was not significant between Guiyang city and Maotai city storerooms, but that in the fungal community was significant. The network analysis revealed that fungal networks were more complex and compact than bacterial networks, and a strong negative correlation existed between bacteria and fungi. Moreover, the bacterial microbiome showed a strong positive association with amylase activity, while the fungal microbiome positively correlated with cellulase activity.ConclusionsThis study demonstrated a significant spatiotemporal heterogeneity in the composition of the microbial community during tobacco aging and highlighted the possible influence of the interactions and enzyme activity on microbial diversity and composition. The findings provided a scientific basis for using microorganisms to regulate and control tobacco aging.