Single-Molecule Real-Time Sequencing to Explore the Mycobiome Diversity in Malt
This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region...
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Published in | Microbiology spectrum Vol. 10; no. 5; p. e0051122 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
1752 N St., N.W., Washington, DC
American Society for Microbiology
26.10.2022
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Abstract | This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans, Aspergillus penicillioides, and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (aw) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products. IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and aw, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases. |
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AbstractList | This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size.
Wickerhamomyces
(56%),
Cyberlindnera
(15%),
Dipodascus
(12%), and
Candida
(6.1%) were characterized as the dominant genera in the raw malts, and
Aspergillus
(35%),
Dipodascus
(21%),
Wickerhamomyces
(11%), and
Candida
(3.5%) in the roasted malts.
Aspergillus proliferans
,
Aspergillus penicillioides
, and
Wickerhamomyces anomalus
represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (a
w
) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products.
IMPORTANCE
Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and a
w
, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases. ABSTRACT This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans, Aspergillus penicillioides, and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (aw) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products. IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and aw, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases. Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. ABSTRACT This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans , Aspergillus penicillioides , and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (a w ) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products. IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and a w , and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases. This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation PacBio-based full-length single-molecule real-time (SMRT) sequencing of the full-length amplicon of the internal transcribed spacer (ITS) region. In total, one kingdom, six phyla, 23 classes, 56 orders, 120 families, 188 genera, 333 species, and 780 operational taxonomic units (OTUs) were detected with satisfactory sequencing depth and sample size. Wickerhamomyces (56%), Cyberlindnera (15%), Dipodascus (12%), and Candida (6.1%) were characterized as the dominant genera in the raw malts, and Aspergillus (35%), Dipodascus (21%), Wickerhamomyces (11%), and Candida (3.5%) in the roasted malts. Aspergillus proliferans, Aspergillus penicillioides, and Wickerhamomyces anomalus represented the crucial biomarkers causing intergroup differences. Correlation analysis regarding environmental factors indicated that the water activity (aw) of the samples affected the composition of the fungal communities in the malts. In practice, special attention should be paid to the mycotoxin-producing fungi, as well as other fungal genera that are inversely correlated with their growth, to ensure the safe use of malt and its end products. IMPORTANCE Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput sequencing (HTS) is beneficial for explaining fungal communities, it presents disadvantages, such as short reads, species-level resolution, and uncertain identification. This work represents the first attempt to characterize the fungal community diversity, with a particular focus on mycotoxin-producing fungi, in malt via the third-generation PacBio-based full-length SMRT sequencing of the ITS region, aiming to explore and compare the differences between the fungal communities of raw and roasted malts. The research is beneficial for developing effective biological control and conservation measures, including improving the roasting conditions, monitoring the environmental humidity and aw, and effectively eliminating and degrading fungi in the industry chain according to the diverse fungal communities determined, for the safe use of malts and their end products, such as beers. In addition, the third-generation SMRT sequencing technology allows highly efficient analysis of fungal community diversity in complex matrices, yielding fast, high-resolution long reads at the species level. It can be extended to different research fields, updating modern molecular methodology and bioinformatics databases. |
Author | Liao, Xiaofang Liu, Jinxin Li, Ying Long, Nan Zhou, Lidong Kong, Weijun Hou, Yujiao Liu, Jiali Shi, Linchun |
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CitedBy_id | crossref_primary_10_3390_foods12081588 crossref_primary_10_3389_fmicb_2024_1394774 crossref_primary_10_1016_j_envres_2023_117977 crossref_primary_10_56294_saludcyt20241064 |
Cites_doi | 10.1038/s41579-018-0116-y 10.1016/j.fm.2019.103378 10.1016/j.foodchem.2020.128744 10.1016/j.ijfoodmicro.2020.108940 10.1111/1758-2229.12776 10.1021/cr050001f 10.1016/j.ijfoodmicro.2021.109428 10.1016/j.lwt.2018.09.001 10.1128/JB.00542-10 10.1016/j.tifs.2019.12.021 10.1007/s00216-013-7516-7 10.1186/s13568-020-01019-1 10.1016/j.foodcont.2020.107141 10.1016/j.microc.2020.105007 10.1007/s12550-014-0202-6 10.1111/jphp.13101 10.1038/nmeth.2604 10.1016/j.meegid.2020.104208 10.1016/B978-0-12-819990-9.00032-9 10.3390/toxins12120789 10.3390/toxins11050301 10.1016/j.eujim.2021.101322 10.1016/j.ijfoodmicro.2017.07.008 10.1016/j.jfca.2021.103997 10.1016/bs.afnr.2019.02.007 10.1016/j.scp.2020.100282 10.1007/s42770-019-00152-9 10.1093/jee/toaa209 10.1038/s41467-021-25641-0 10.1016/j.heliyon.2020.e04606 10.1016/j.ecoenv.2015.06.002 10.3389/fmicb.2021.678250 10.3390/toxins12100656 10.1016/j.funeco.2021.101062 10.1016/j.agee.2016.03.030 10.1016/j.cofs.2021.07.003 10.1038/ismej.2015.249 10.1128/mSphere.00741-19 10.3389/fmicb.2021.684386 10.1016/j.foodchem.2021.130926 10.1016/j.ijfoodmicro.2018.03.005 10.1093/nar/gky066 10.1007/s00284-017-1400-1 10.1016/j.ygeno.2021.11.014 10.1002/jsfa.4112 10.1038/s41467-019-13036-1 10.1016/j.foodres.2018.07.024 |
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Keywords | single-molecule real-time sequencing toxigenic fungi full-length ITS fungal community mycobiome diversity malt |
Language | English |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Nan Long and Jinxin Liu contributed equally to this work. Author order was determined by drawing straws. The authors declare no conflict of interest. |
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Snippet | This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the third-generation... Fungal contamination and secondary metabolite accumulation in agricultural products represent a global food safety challenge. Although high-throughput... ABSTRACT This study determined the composition of fungal communities and characterized the enriched fungal species in raw and roasted malts via the... |
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SubjectTerms | Food Microbiology full-length ITS fungal community malt mycobiome diversity Research Article single-molecule real-time sequencing toxigenic fungi |
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Title | Single-Molecule Real-Time Sequencing to Explore the Mycobiome Diversity in Malt |
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