Assessment of the Microbiome and Potential Aflatoxin Associated With the Medicinal Herb Platycladus orientalis

Variations of the fungal microbiome in Corydalis Rhizoma with different collection areas, processing methods, and storage conditions

Corydalis Rhizoma (CR, Yanhusuo in Chinese) has been widely used as an analgesic in herbal medicine and functional food. Cases of fungal and mycotoxin contamination in CR have been reported. In this study, the composition and diversity of fungal microbiome in CR samples from four herbal markets and two processing methods were investigated by DNA metabarcoding. Variations of the fungal microbiome in CR during cold and conventional storage were monitored. Results showed that Aspergillus was the dominant genus and saprotroph was the dominant trophic mode. Six potential toxigenic fungi, namely, Aspergillus fumigatus, Aspergillus ostianus, Aspergillus terreus, Penicillium citrinum, Penicillium oxalicum, and Trichothecium roseum, were detected. Differences in fungal composition and diversity among various groups based on collection areas and processing methods were also observed. Moreover, the relative abundance of dominant genera in CR samples stored at different temperatures was significantly different and changed with storage time. This study is the first to reveal the influence of collection areas, processing methods, and storage conditions on the fungal microbiome in CR, which was expected to provide a basis for control strategies of fungal contamination in the industrial chain of CR.

Influence of sampling location and processing on the assembly and network of Polygoni Multiflori Radix surface microbiome

The raw and processed roots of Polygonum multiflorum Thunb is a popular traditional Chinese medicine. However, Polygoni Multiflori Radix is easily contaminated by toxigenic fungi and mycotoxins during harvesting, processing, and transportation, thereby posing a health risk for consumers. This study aims to investigate the presence of fungi on the surface of raw and processed Polygoni Multiflori Radix collected from four producing areas using high-throughput sequencing. Results showed that the phyla Ascomycota and Basidiomycota, the genera Xeromyces, Cystofilobasidium, Eurotium, and Aspergillus were the dominant fungus, and significant differences are presented in four areas and two processed products. Three potential mycotoxin-producing fungi were detected, namely Trichosporon cutaneum, Aspergillus restrictus, and Fusarium oxysporum. The α-diversity and network complexity showed significant differences in four areas. Chao 1 and Shannon were highest in Yunnan (YN), then incrementally decreased from SC (Sichuan) to AH (Anhui) and GD (Guangdong) areas. Meanwhile, α-diversity was also strongly influenced by processing. Chao 1 and Shannon indices were higher in the raw group, however, the network complexity and connectivity were higher in the processed group. In conclusion, the assembly and network of the surface microbiome on Polygoni Multiflori Radix were influenced by sampling location and processing. This work provides details on the surface microbiome of Polygoni Multiflori Radix samples, which could ensure the drug and consumers' safety.

DNA metabarcoding analysis of fungal community on surface of four root herbs

Objective

Angelicae Sinensis Radix (ASR, Danggui in Chinese), Cistanches Herba (CH, Roucongrong in Chinese), Ginseng Radix et Rhizoma (PG, Renshen in Chinese), and Panacis Quinquefolii Radix (PQ, Xiyangshen in Chinese), widely used as medicine and dietary supplement around the world, are susceptible to fungal and mycotoxin contamination. In this study, we aim to analyze their fungal community by DNA metabarcoding.

Methods

A total of 12 root samples were collected from three main production areas in China. The samples were divided into four groups based on herb species, including ASR, CH, PG, and PQ groups. The fungal community on the surface of four root groups was investigated through DNA metabarcoding via targeting the internal transcribed spacer 2 region (ITS2).

Results

All the 12 samples were detected with fungal contamination. Rhizopus (13.04%-74.03%), Aspergillus (1.76%-23.92%), and Fusarium (0.26%-15.27%) were the predominant genera. Ten important fungi were identified at the species level, including two potential toxigenic fungi (Penicillium citrinum and P. oxalicum) and eight human pathogenic fungi (Alternaria infectoria, Candida sake, Hyphopichia burtonii, Malassezia globosa, M. restricta, Rhizopus arrhizus, Rhodotorula mucilaginosa, and Ochroconis tshawytschae). Fungal community in ASR and CH groups was significantly different from other groups, while fungal community in PG and PQ groups was relatively similar.

Conclusion

DNA metabarcoding revealed the fungal community in four important root herbs. This study provided an important reference for preventing root herbs against fungal and mycotoxin contamination.

DNA Metabarcoding Reveals the Fungal Community on the Surface of Lonicerae Japonicae Flos, an Edible and Medicinal Herb

Lonicerae Japonicae Flos (LJF) has been globally applied as an herbal medicine and tea. A number of reports recently revealed fungal and mycotoxin contamination in medicinal herbs. It is essential to analyze the fungal community in LJF to provide an early warning for supervision. In this study, the fungal community in LJF samples was identified through DNA metabarcoding. A total of 18 LJF samples were collected and divided based on the collection areas and processing methods. The results indicated that Ascomycota was the dominant phylum. At the genus level, Rhizopus was the most abundant, followed by Erysiphe and Fusarium. Ten pathogenic fungi were detected among the 41 identified species. Moreover, Rhizopus, Fusarium, and Aspergillus had lower relative abundances in LJF samples under oven drying than under other processing methods. This work is expected to provide comprehensive knowledge of the fungal community in LJF and a theoretical reference for enhanced processing methods in practical manufacturing.

Occurrence of fungi and mycotoxins in herbal medicines and rapid detection of toxin-producing fungi

Contamination from external hazardous materials may greatly influence the safety and efficacy of herbal medicines. This paper aimed to evaluate the levels of contamination by mycotoxins and toxigenic fungi in herbal medicines and establish a rapid method for detecting toxin-producing fungi. Herein, 62.92%, 36.25%, and 64.17% of herbal medicines were contaminated by aflatoxins (AFs), ochratoxins, and fumonisins, respectively. Aspergillus (43.77%), Fusarium (5.17%), and Cladosporium (4.46%) were the three predominant genera. Spearman's correlation results showed that Aspergillus and Fusarium were significantly and positively correlated with mycotoxin content (R > 0.5, P < 0.05). In addition, 323 fungal strains were isolated from herbal medicines, and 20 species were identified, mainly belonging to Aspergillus and Penicillium. Analysis of potential mycotoxin-producing fungi showed that Aspergillus flavus can produce AFs, and Aspergillus ochraceus and Aspergillus niger can produce ochratoxin A (OTA). Multiplex real-time polymerase chain reaction showed that A. flavus harbored AF synthesis genes (aflR), and A. ochraceus and A. niger harbored OTA synthesis genes (aoksl). With these synthesis genes, 67.07% and 37.20% of 164 herbal medicines were positive for toxigenic genes. Furthermore, an excellent correlation was found between the above gene copies and mycotoxin content (R2 = 0.99). Our results confirmed the high detection rate of mycotoxins in herbal medicines and identified pivotal AF- and OTA-producing fungi. In conclusion, this paper provided the contamination status of fungi and mycotoxins in herbal medicines and established a rapid method for detecting toxigenic fungi.

Fungal microbiome related to mycotoxin contamination in medicinal and edible seed Semen Persicae

Medicinal and edible seed Semen Persicae is susceptible to mycotoxin and fungal contamination. However, the occurrence of mycotoxin contamination and fungal infection is still unclear. In this paper, ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry and high-throughput sequencing were conducted to determine the mycotoxin contents and fungal abundances of Semen Persicae. 42.86% of samples were positive for aflatoxin B1 (26.48-48.37 μg/kg) and 28.57% of samples were positive for aflatoxin B2 (1.47-4.82 μg/kg). Ochratoxin A and fumonisin B1 were only detected in one sample (91.02 and 34.61 μg/kg, respectively). Chao 1 and Shannon indices were significantly higher in the Dalian of Liaoning, Baotou of Innermongolia and Langfang of Hebei regions than in other groups. Ascomycota, Basidiomycota, Wallemia, Candica, Saccharomyces and Aspergillus were the predominant fungi and they were significantly region-specific. Simultaneously, the diversity, composition and co-occurrence network complexity in the mycotoxin-free group were significantly higher than those in the mycotoxin-contaminated group. Spearman correlation analysis showed aflatoxins, ochratoxin A and fumonisins contents were positively and significantly correlated with the abundances of Aspergillus, Rhodotorula, Wallemia and Candida. In conclusion, this study reported the prevalence of mycotoxin contamination and the great diversity of fungi associated with Semen Persicae for the first time, providing an early warning for subsequent potential mycotoxin biosynthesis.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Sampling locations and processing methods shape fungi microbiome on the surface of edible and medicinal Arecae semen

Introduction

Arecae semen, which is derived from the dried ripe seed of Areca catechu L., has been commonly used as one of the major traditional Chinese medicines (TCMs). Three types of crude herbal preparations, namely, raw Arecae semen (AS), Arecae semen tostum (SAS), and Arecae semen carbonisata (FAS), are available for different clinical applications in TCMs. Although aflatoxin contamination in Arecae semen has been reported preliminarily, only a few studies have been conducted on fungal contamination.

Methods

In this study, the presence of fungi on the surface of three Arecae semen (AS, SAS, and FAS) that collected from four provinces were investigated using high-throughput sequencing and internal transcribed spacer 2.

Results

Results showed that the phyla Ascomycota (75.45%) and Basidiomycota (14.29%) and the genera Wallemia (7.56%), Botryosphaeria (6.91%), Davidiella (5.14%), and Symbiotaphrina (4.87%) were the dominant fungi, and they presented significant differences in four areas and three processed products (p < 0.05). The α-diversity and network complexity exhibited significant differences in the four sampling locations (p < 0.05), with higher in Yunnan (Chao 1, 213.45; Shannon, 4.61; average degree, 19.96) and Hainan (Chao 1, 198.27; Shannon, 4.21; average degree, 22.46) provinces. Significant differences were noted in the three processed samples; and SAS group had highest α-diversity (Chao 1, 167.80; Shannon, 4.54) and network complexity (average degree, 18.32).

Conclusions

In conclusion, the diversity and composition of microbiome on the surface of Arecae semen were shaped by sampling location and processing methods. This work provides details on the surface microbiome of Arecae semen samples and highlights the importance of roles of origin and processing methods in microbiomes, ensuring drug efficacy and food safety.

Characterization of the Fungal Community in Fritillariae Cirrhosae Bulbus through DNA Metabarcoding

Fritillariae Cirrhosae Bulbus (FCB) is a well-known and precious traditional Chinese medicine with a medicinal history spanning thousands of years. In recent years, it has been reported that fungal and mycotoxin contamination influenced the safety and quality of FCB. It is essential to systematically study the fungal community for the early warning of fungal and mycotoxin contamination in this herb. A total of 15 FCB samples were collected from five provinces in China, and the fungal communities in the FCB samples were analyzed via amplifying the internal transcribed spacer 2 region through the Illumina Miseq PE300 platform. Furthermore, we compared the differences in fungal community in five groups based on collection areas. Results showed that Ascomycota (41.58-99.66%) and Mucoromycota (0-57.42%) were dominant at the phylum level. Eurotiomycetes (8.49-63.93%), Eurotiales (8.49-63.53%), and Aspergillaceae (8.49-63.51%) were the most abundant at the class, order, and family levels. Aspergillus (8.49-63.41%), Rhizopus (0-57.42%), Fusarium (0-22.81%), Cladosporium (0.16-9.14%), and Alternaria (0.06-17.95%) were the main genera in FCB samples. A total of 34 fungal taxa were identified at the species level, including five potentially toxigenic fungi namely Penicillium brevicompactum, P. citrinum, P. oxalicum, Trichothecium roseum, and Aspergillus restrictus. The differences in fungal community between the five groups were observed. Our findings provide references for the safe utilization and quality improvement of FCB.

Analysis of Fungal Microbiomes in Edible Medicinal Morindae Officinalis Radix and Alpiniae Oxyphyllae Fructus Using DNA Metabarcoding

Morindae Officinalis Radix (MOR) and Alpiniae Oxyphyllae Fructus (AOF) have been widely used as dietary supplements and traditional herbal medicines for centuries. Fungal and mycotoxin contamination in MOR and AOF has been reported recently. In this study, fungi in MOR and AOF are first investigated using DNA metabarcoding, and the differences in fungal microbiome between moldy and non−moldy samples are analyzed. The results show that Ascomycota is the most prevailing fungus at the phylum level in MOR and AOF with relative abundances of 49.53–94.32% and 14.81–81.85%, respectively. Penicillium (1.86–76.14%), Cladosporium (1.82–56.65%), and Trichoderma (0.12–19.71%) are the dominant genera in MOR. Penicillium (0.27–56.06%), Papiliotrema (0.04–51.71%), and Cladosporium (3.08–44.41%) are the dominant genera in AOF. Two potential toxigenic fungi were detected, namely, Trichoderma atroviride and Fusarium equiseti. Moreover, the differences in fungal communities between moldy and non−moldy samples were monitored. In conclusion, DNA metabarcoding can be used to assess the fungal microbiome in edible medicinal herbs, thereby providing a basis for ensuring food safety and drug efficacy.

Investigation of fungal contamination in medicinal and edible Lycii Fructus through DNA metabarcoding

AIMS

Lycii Fructus (LF) is considered as a 'superfood' due to its health benefits and delicious tastes, which has gained popularity worldwide. However, LF is also a proper host for fungal growth due to its abundant nutrients. Fungal contamination seriously affects the quality and safety of LF and poses threats to consumer health.

METHODS AND RESULTS

In this study, a total of 15 LF samples were collected from five provinces in China, and were divided into five groups based on the collection areas. Fungal contamination in LF was investigated by targeting the internal transcribed spacer 2 region using Illumina Miseq PE300 platform, and the differences of fungal community in groups based on collection areas were compared. Results showed that the fungal contamination was detected in all the 15 LF samples. Ascomycota, Dothideomycetes, Pleosporales and Pleosporaceae were dominant at the phylum, class, order and family levels, respectively. At the genus level, Alternaria, Cladosporium and Fusarium were the three dominant genera. In all, 24 fungal species were identified. Among which, two species, namely Penicillium oxalicum and Trichothecium roseum, were potentially toxigenic.

CONCLUSIONS

All 15 LF samples were detected with fungal contamination. The differences of fungal community in LF samples collected from different areas were observed. DNA metabarcoding was demonstrated as an efficient method to monitor the fungal contamination in LF.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work comprehensively reveals the fungal diversity and composition in LF and provides early warning for potential mycotoxin contamination.