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Chetty A, Blekhman R. Multi-omic approaches for host-microbiome data integration. Gut Microbes 2024; 16:2297860. [PMID: 38166610 PMCID: PMC10766395 DOI: 10.1080/19490976.2023.2297860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
The gut microbiome interacts with the host through complex networks that affect physiology and health outcomes. It is becoming clear that these interactions can be measured across many different omics layers, including the genome, transcriptome, epigenome, metabolome, and proteome, among others. Multi-omic studies of the microbiome can provide insight into the mechanisms underlying host-microbe interactions. As more omics layers are considered, increasingly sophisticated statistical methods are required to integrate them. In this review, we provide an overview of approaches currently used to characterize multi-omic interactions between host and microbiome data. While a large number of studies have generated a deeper understanding of host-microbiome interactions, there is still a need for standardization across approaches. Furthermore, microbiome studies would also benefit from the collection and curation of large, publicly available multi-omics datasets.
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Affiliation(s)
- Ashwin Chetty
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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2
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Avisar D, Azulay S, Bombonato L, Carvalho D, Dallapicolla H, de Souza C, Dos Santos A, Dias T, Galan MP, Galvao M, Gonsalves JM, Gonzales E, Graça R, Livne S, Mafia R, Manoeli A, May M, Menezes TRD, Pinheiro AC, Porto A, Rocha C, Schafer A, Schafer B, Zauza E, Silva W. Safety Assessment of the CP4 EPSPS and NPTII Proteins in Eucalyptus. GM CROPS & FOOD 2023; 14:1-14. [PMID: 37334790 DOI: 10.1080/21645698.2023.2222436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Glyphosate herbicide treatment is essential to sustainable Eucalyptus plantation management in Brazil. Eucalyptus is highly sensitive to glyphosate, and Suzano/FuturaGene has genetically modified eucalyptus to tolerate glyphosate, with the aim of both protecting eucalyptus trees from glyphosate application damage and improving weed management. This study presents the biosafety results of the glyphosate-tolerant eucalyptus event 751K032, which expresses the selection marker neomycin phosphotransferase II (NPTII) enzyme and CP4-EPSPS, a glyphosate-tolerant variant of plant 5-enolpyruvyl-shikimate-3-phosphate synthase enzyme. The transgenic genetically modified (GM) event 751K032 behaved in the plantations like conventional non-transgenic eucalyptus clone, FGN-K, and had no effects on arthropods and soil microorganisms. The engineered NPTII and CP4 EPSPS proteins were heat-labile, readily digestible, and according to the bioinformatics analyses, unlikely to cause an allergenic or toxic reaction in humans or animals. This assessment of the biosafety of the glyphosate-tolerant eucalyptus event 751K032 concludes that it is safe to be used for wood production.
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Affiliation(s)
| | | | - Lorena Bombonato
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | - Denise Carvalho
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | - Carla de Souza
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | - Tatiane Dias
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | - Milton Galvao
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | - Esteban Gonzales
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | - Rodrigo Graça
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | | | | | - Mike May
- R&D, FuturaGene Israel Ltd, Rehovot, Israel
| | | | | | - Antonio Porto
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | - Carolina Rocha
- Suzano S.A. (FuturaGene - Biotech Division), Itapetininga, Brazil
| | | | | | | | - William Silva
- W J Silva Consultoria Agricola S/C LTDA, Jardinópolis, Brazil
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3
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Alleyne A, Mason S, Vallès Y. Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease. J Fungi (Basel) 2023; 9:1130. [PMID: 38132731 PMCID: PMC10743849 DOI: 10.3390/jof9121130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.
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Affiliation(s)
- Angela Alleyne
- Faculty of Science and Technology, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados (Y.V.)
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4
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Hlangwani E, Abrahams A, Masenya K, Adebo OA. Analysis of the bacterial and fungal populations in South African sorghum beer (umqombothi) using full-length 16S rRNA amplicon sequencing. World J Microbiol Biotechnol 2023; 39:350. [PMID: 37864040 PMCID: PMC10589195 DOI: 10.1007/s11274-023-03764-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/14/2023] [Indexed: 10/22/2023]
Abstract
There is a need to profile microorganisms which exist pre-and-post-production of umqombothi, to understand its microbial diversity and the interactions which subsequently influence the final product. Thus, this study sought to determine the relative microbial abundance in umqombothi and predict the functional pathways of bacterial and fungal microbiota present. Full-length bacterial 16S rRNA and internal transcribed spacer (ITS) gene sequencing using PacBio single-molecule, real-time (SMRT) technology was used to assess the microbial compositions. PICRUSt2 was adopted to infer microbial functional differences. A mixture of harmful and beneficial microorganisms was observed in all samples. The microbial diversity differed significantly between the mixed raw ingredients (MRI), customary beer brew (CB), and optimised beer brew (OPB). The highest bacterial species diversity was observed in the MRI, while the highest fungal species diversity was observed in the OPB. The dominant bacterial species in the MRI, CB, and OPB were Kosakonia cowanii, Apilactobacillus pseudoficulneus, and Vibrio alginolyticus, respectively, while the dominant fungal species was Apiotrichum laibachii. The predicted functional annotations revealed significant (p < 0.05) differences in the microbial pathways of the fermented and unfermented samples. The most abundant pathways in the MRI were the branched-chain amino acid biosynthesis super pathway and the pentose phosphate pathway. The CB sample was characterised by folate (vitamin B9) transformations III, and mixed acid fermentation. Biotin (vitamin B7) biosynthesis I and L-valine biosynthesis characterised the OPB sample. These findings can assist in identifying potential starter cultures for the commercial production of umqombothi. Specifically, A. pseudoficulneus can be used for controlled fermentation during the production of umqombothi. Likewise, the use of A. laibachii can allow for better control over the fermentation kinetics such as carbohydrate conversion and end-product characteristics, especially esters and aroma compounds.
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Affiliation(s)
- Edwin Hlangwani
- Food Innovation Research Group, Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa
| | - Adrian Abrahams
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa
| | - Kedibone Masenya
- Neuroscience Institute, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
| | - Oluwafemi Ayodeji Adebo
- Food Innovation Research Group, Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg, South Africa.
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5
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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Quantifying Trade-Offs in the Choice of Ribosomal Barcoding Markers for Fungal Amplicon Sequencing: a Case Study on the Grapevine Trunk Mycobiome. Microbiol Spectr 2022; 10:e0251322. [PMID: 36409146 PMCID: PMC9769941 DOI: 10.1128/spectrum.02513-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology and multiplexing has rapidly expanded our ability to characterize fungal diversity in the environment. However, obtaining an unbiased assessment of the fungal community using ribosomal markers remains challenging. Longer amplicons were shown to improve taxonomic resolution and resolve ambiguities by reducing the risk of spurious operational taxonomic units. We examined the implications of barcoding strategies by amplifying and sequencing two ribosomal DNA fragments. We analyzed the performance of the full internal transcribed spacer (ITS) and a longer fragment including also a part of the 28S ribosomal subunit replicated on 60 grapevine trunk core samples. Grapevine trunks harbor highly diverse fungal communities with implications for disease development. Using identical handling, amplification, and sequencing procedures, we obtained higher sequencing depths for the shorter ITS amplicon. Despite the more limited access to polymorphism, the overall diversity in amplified sequence variants was higher for the shorter ITS amplicon. We detected no meaningful bias in the phylogenetic composition due to the amplicon choice across analyzed samples. Despite the increased resolution of the longer ITS-28S amplicon, the higher and more consistent yields of the shorter amplicons produced a clearer resolution of the fungal community of grapevine stem samples. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals. IMPORTANCE Surveying fungal communities is key to our understanding of ecological functions of diverse habitats. Fungal communities can inform about the resilience of agricultural ecosystems, risks to human health, and impacts of pathogens. Community compositions are typically analyzed using ribosomal DNA sequences. Due to technical limitations, most fungal community surveys were based on amplifying a short but highly variable fragment. Advances in sequencing technology enabled the use of longer fragments that can address some limitations of species identification. In this study, we examined the implications of choosing either a short or long ribosomal sequence fragment by replicating the analyses on 60 grapevine wood core samples. Using highly accurate long-read sequencing, we found that the shorter fragment produced substantially higher yields. The shorter fragment also revealed more sequence and species diversity. Our study highlights that the choice of ribosomal amplicons should be carefully evaluated and adjusted according to specific goals.
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Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome. mSystems 2022; 7:e0012022. [PMID: 35862808 PMCID: PMC9426494 DOI: 10.1128/msystems.00120-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.
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Pérez-Losada M, Narayanan DB, Kolbe AR, Ramos-Tapia I, Castro-Nallar E, Crandall KA, Domínguez J. Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes. Front Microbiol 2022; 13:854423. [PMID: 35620097 PMCID: PMC9127802 DOI: 10.3389/fmicb.2022.854423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/21/2022] [Indexed: 11/21/2022] Open
Abstract
The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, The George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Dhatri Badri Narayanan
- Computational Biology Institute, The George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Allison R Kolbe
- Computational Biology Institute, The George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Ignacio Ramos-Tapia
- Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Eduardo Castro-Nallar
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile.,Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Chile
| | - Keith A Crandall
- Computational Biology Institute, The George Washington University, Washington, DC, United States.,Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Jorge Domínguez
- Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, Vigo, Spain
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Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio 2022; 13:e0244421. [PMID: 35404122 PMCID: PMC9040722 DOI: 10.1128/mbio.02444-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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10
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Del Álamo AC, Pariente MI, Molina R, Martínez F. Advanced bio-oxidation of fungal mixed cultures immobilized on rotating biological contactors for the removal of pharmaceutical micropollutants in a real hospital wastewater. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:128002. [PMID: 34896717 DOI: 10.1016/j.jhazmat.2021.128002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/11/2021] [Accepted: 12/04/2021] [Indexed: 05/25/2023]
Abstract
Hospital wastewater represents an important source of pharmaceutical active compounds (PhACs) as contaminants of emerging concern for urban wastewater treatment plants. This work evaluates a fungal biological treatment of a hospital effluent before discharging in the municipal sewer system. This treatment was performed in rotating biological contactors (RBCs) covered with wooden planks in order to promote the attachment of the fungal biomass. These bioreactors, initially inoculated with Trametes versicolor as white rot fungi, have created biofilms of a diversified population of fungal (wood-decaying fungi belonging to Basidiomycota and Ascomycetes) and bacterial (Beta-proteobacteria, Firmicutes, and Acidobacteria) microorganisms. The mixed fungal/bacterial community achieved a stable performance in terms of carbon, nitrogen, and phosphorous reductions for 75 days of continuous operation. Moreover, a remarkable removal of pharmaceutical micropollutants was accomplished especially for antibiotics (98.4 ± 0.7, 83 ± 8% and 76 ± 10 for azithromycin, metronidazole and sulfamethoxazole, respectively). Previous studies have proven a high efficiency of fungi for the removal of microcontaminants as a result of advanced bio-oxidation processes mediated by oxidizing hydroxyl radicals. This study evidences the development of a stable fungal-bacterial mixed culture over wooden-modified RBCs for in-situ removal of pharmaceutical compounds of hospital wastewater under non-sterile conditions and non-strict temperature control, avoiding periodical fungal inoculation due to destabilization and displacement of fungal cultures by indigenous wastewater bacteria.
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Affiliation(s)
- A Cruz Del Álamo
- Department of Chemical and Environmental Technology, Rey Juan Carlos University, Móstoles, Spain
| | - M I Pariente
- Department of Chemical and Environmental Technology, Rey Juan Carlos University, Móstoles, Spain
| | - R Molina
- Department of Chemical and Environmental Technology, Rey Juan Carlos University, Móstoles, Spain.
| | - F Martínez
- Department of Chemical and Environmental Technology, Rey Juan Carlos University, Móstoles, Spain
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11
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Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci Rep 2021; 11:24241. [PMID: 34930992 PMCID: PMC8688430 DOI: 10.1038/s41598-021-03733-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022] Open
Abstract
Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the effectiveness of using riverine water eDNA to simultaneously monitor the riverine and terrestrial biodiversity information remains unidentified. Here, we proposed that the monitoring effectiveness could be approximated by the transportation effectiveness of land-to-river and upstream-to-downstream biodiversity information flows and described by three new indicators. Subsequently, we conducted a case study in a watershed on the Qinghai-Tibet Plateau. The results demonstrated that there was higher monitoring effectiveness on summer or autumn rainy days than in other seasons and weather conditions. The monitoring of the bacterial biodiversity information was more efficient than the monitoring of the eukaryotic biodiversity information. On summer rainy days, 43-76% of species information in riparian sites could be detected in adjacent riverine water eDNA samples, 92-99% of species information in riverine sites could be detected in a 1-km downstream eDNA sample, and half of dead bioinformation (the bioinformation labeling the biological material that lacked life activity and fertility) could be monitored 4-6 km downstream for eukaryotes and 13-19 km downstream for bacteria. The current study provided reference method and data for future monitoring projects design and for future monitoring results evaluation.
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12
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Tedersoo L, Mikryukov V, Anslan S, Bahram M, Khalid AN, Corrales A, Agan A, Vasco-Palacios AM, Saitta A, Antonelli A, Rinaldi AC, Verbeken A, Sulistyo BP, Tamgnoue B, Furneaux B, Ritter CD, Nyamukondiwa C, Sharp C, Marín C, Dai DQ, Gohar D, Sharmah D, Biersma EM, Cameron EK, De Crop E, Otsing E, Davydov EA, Albornoz FE, Brearley FQ, Buegger F, Gates G, Zahn G, Bonito G, Hiiesalu I, Hiiesalu I, Zettur I, Barrio IC, Pärn J, Heilmann-Clausen J, Ankuda J, Kupagme JY, Sarapuu J, Maciá-Vicente JG, Fovo JD, Geml J, Alatalo JM, Alvarez-Manjarrez J, Monkai J, Põldmaa K, Runnel K, Adamson K, Bråthen KA, Pritsch K, Tchan KI, Armolaitis K, Hyde KD, Newsham KK, Panksep K, Adebola LA, Lamit LJ, Saba M, da Silva Cáceres ME, Tuomi M, Gryzenhout M, Bauters M, Bálint M, Wijayawardene N, Hagh-Doust N, Yorou NS, Kurina O, Mortimer PE, Meidl P, Nilsson RH, Puusepp R, Casique-Valdés R, Drenkhan R, Garibay-Orijel R, Godoy R, Alfarraj S, Rahimlou S, Põlme S, Dudov SV, Mundra S, Ahmed T, Netherway T, Henkel TW, Roslin T, Fedosov VE, Onipchenko VG, Yasanthika WAE, Lim YW, Piepenbring M, Klavina D, Kõljalg U, Abarenkov K. The Global Soil Mycobiome consortium dataset for boosting fungal diversity research. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00493-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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d'Entremont TW, Migicovsky Z, López-Gutiérrez JC, Walker AK. Saltmarsh rhizosphere fungal communities vary by sediment type and dominant plant species cover in Nova Scotia, Canada. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:458-463. [PMID: 33185975 DOI: 10.1111/1758-2229.12904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 05/06/2023]
Abstract
We surveyed Spartina saltmarsh sediment rhizosphere fungal communities at three saltmarshes and two timepoints in coastal Nova Scotia. Based on ITS2 Illumina miSeq rDNA data and multivariate analysis, neither sediment zone nor collection period correlated with fungal ASV richness, but collection site did. However, Shannon diversity indicated that sediment zone played a significant role in fungal diversity. For unweighted and weighted UniFrac distance, site was the major factor driving beta-diversity, with sediment zone and collection period having smaller roles. Sediment type and saltmarsh plant species may play important roles in structuring rhizosphere fungal assemblages, here dominated by ascomycetes. To our knowledge, our study is the first to assess fungal sediment communities in saltmarshes in Atlantic Canada using metabarcoding. It provides a biodiversity analysis of sediment fungi in a poorly studied but highly important ecosystem and points to their roles in nutrient cycling, blue carbon, coastal stability and coastal restoration. Our work will inform ongoing saltmarsh restoration in Atlantic Canada.
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Affiliation(s)
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | | | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
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14
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Kolaříková Z, Slavíková R, Krüger C, Krüger M, Kohout P. PacBio sequencing of Glomeromycota rDNA: a novel amplicon covering all widely used ribosomal barcoding regions and its applicability in taxonomy and ecology of arbuscular mycorrhizal fungi. THE NEW PHYTOLOGIST 2021; 231:490-499. [PMID: 33780549 DOI: 10.1111/nph.17372] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 03/23/2021] [Indexed: 05/02/2023]
Abstract
There is no consensus barcoding region for determination of arbuscular mycorrhizal fungal (AMF) taxa. To overcome this obstacle, we have developed an approach to sequence an AMF marker within the ribosome-encoding operon (rDNA) that covers all three widely applied variable molecular markers. Using a nested PCR approach specific to AMF, we amplified a part (c. 2.5 kb) of the rDNA spanning the majority of the small subunit rRNA (SSU) gene, the complete internal transcribed spacer (ITS) region and a part of the large subunit (LSU) rRNA gene. The PCR products were sequenced on the PacBio platform utilizing Single Molecule Real Time (SMRT) sequencing. Employing this method for selected environmental DNA samples, we were able to describe complex AMF communities consisting of various glomeromycotan lineages. We demonstrate the applicability of this new 2.5 kb approach to provide robust phylogenetic assignment of AMF lineages without known sequences from pure cultures and to consolidate information about AMF taxon distributions coming from three widely used barcoding regions into one integrative dataset.
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Affiliation(s)
- Zuzana Kolaříková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Renata Slavíková
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Claudia Krüger
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Manuela Krüger
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
| | - Petr Kohout
- Institute of Botany of the Czech Academy of Sciences, Průhonice, CZ-252 43, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, CZ-128 44, Czech Republic
- Institute of Microbiology of the Czech Academy of Sciences, Prague, CZ-142 20, Czech Republic
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15
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Furneaux B, Bahram M, Rosling A, Yorou NS, Ryberg M. Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Mol Ecol Resour 2021; 21:1833-1849. [PMID: 33811446 DOI: 10.1111/1755-0998.13387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/19/2021] [Accepted: 03/01/2021] [Indexed: 01/04/2023]
Abstract
Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
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Affiliation(s)
- Brendan Furneaux
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Anna Rosling
- Program in Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Nourou S Yorou
- Research Unit in Tropical Mycology and Plant-Fungi Interactions, LEB, University of Parakou, Parakou, Benin
| | - Martin Ryberg
- Program in Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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16
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Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B, Yin J, Gao N, Shen W, Schnabl B. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021; 11:530. [PMID: 33918473 PMCID: PMC8066849 DOI: 10.3390/biom11040530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.
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Affiliation(s)
- Bei Gao
- Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
| | - Pengcheng Tu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China;
| | - Bing Li
- Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China;
| | - Jun Yin
- Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Nan Gao
- Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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Hill R, Llewellyn T, Downes E, Oddy J, MacIntosh C, Kallow S, Panis B, Dickie JB, Gaya E. Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives. Front Microbiol 2021; 12:643731. [PMID: 33841366 PMCID: PMC8024981 DOI: 10.3389/fmicb.2021.643731] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Seed banks were first established to conserve crop genetic diversity, but seed banking has more recently been extended to wild plants, particularly crop wild relatives (CWRs) (e.g., by the Millennium Seed Bank (MSB), Royal Botanic Gardens Kew). CWRs have been recognised as potential reservoirs of beneficial traits for our domesticated crops, and with mounting evidence of the importance of the microbiome to organismal health, it follows that the microbial communities of wild relatives could also be a valuable resource for crop resilience to environmental and pathogenic threats. Endophytic fungi reside asymptomatically inside all plant tissues and have been found to confer advantages to their plant host. Preserving the natural microbial diversity of plants could therefore represent an important secondary conservation role of seed banks. At the same time, species that are reported as endophytes may also be latent pathogens. We explored the potential of the MSB as an incidental fungal endophyte bank by assessing diversity of fungi inside stored seeds. Using banana CWRs in the genus Musa as a case-study, we sequenced an extended ITS-LSU fragment in order to delimit operational taxonomic units (OTUs) and used a similarity and phylogenetics approach for classification. Fungi were successfully detected inside just under one third of the seeds, with a few genera accounting for most of the OTUs-primarily Lasiodiplodia, Fusarium, and Aspergillus-while a large variety of rare OTUs from across the Ascomycota were isolated only once. Fusarium species were notably abundant-of significance in light of Fusarium wilt, a disease threatening global banana crops-and so were targeted for additional sequencing with the marker EF1α in order to delimit species and place them in a phylogeny of the genus. Endophyte community composition, diversity and abundance was significantly different across habitats, and we explored the relationship between community differences and seed germination/viability. Our results show that there is a previously neglected invisible fungal dimension to seed banking that could well have implications for the seed collection and storage procedures, and that collections such as the MSB are indeed a novel source of potentially useful fungal strains.
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Affiliation(s)
- Rowena Hill
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Theo Llewellyn
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Elizabeth Downes
- Department for Environment, Food and Rural Affairs, London, United Kingdom
| | - Joseph Oddy
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Catriona MacIntosh
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Simon Kallow
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
- Division of Crop Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven, Leuven, Belgium
| | - Bart Panis
- Bioversity International, Montpellier, France
| | - John B. Dickie
- Collections Department, Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, United Kingdom
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Cason ED, Mahlomaholo BJ, Taole MM, Abong GO, Vermeulen JG, de Smidt O, Vermeulen M, Steyn L, Valverde A, Viljoen B. Bacterial and Fungal Dynamics During the Fermentation Process of Sesotho, a Traditional Beer of Southern Africa. Front Microbiol 2020; 11:1451. [PMID: 32695089 PMCID: PMC7339052 DOI: 10.3389/fmicb.2020.01451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/04/2020] [Indexed: 12/21/2022] Open
Abstract
Sesotho is an indigenous cereal-based fermented drink traditionally produced in the mountain kingdom of Lesotho, Southern Africa. The present study sought to examine the microbial (bacterial and fungal) community composition of Sesotho at five fermentation stages in five different locations. Using culture-independent (Illumina sequencing) techniques it was found that the bacterial communities followed similar successional patterns during the fermentation processes, regardless of geographical location and recipe variation between breweries. The most abundant bacterial taxa belonged to the phyla Firmicutes (66.2% of the reads on average) and Proteobacteria (22.1%); the families Lactobacillaceae (54.9%), Enterobacteriaceae (14.4%) and Leoconostrocaceae (8.1%); and the genera Lactobacillus (54%), Leuconostoc (10.7%), Leptotrichia (8.5%), and Weissella (5.5%). Most fungal taxa were from the phyla Ascomycota (60.7%) and Mucoromycota (25.3%); the families Rhizopodaceae (25.3%), Nectriaceae (24.2%), Saccharomycetaceae (16%) and Aspergillaceae (6.7%); and the genera Rhizopus (25.3%), Saccharomyces (9.6%), and Aspergillus (2.5%). Lactic acid bacteria (LAB) such as Enterococcus, Pediococcus, Lactobacillus, Leuconostoc, and Wiesella; as well as yeasts belonging to the genus Saccharomyces, were dominant in all breweries during the production of Sesotho. Several pathogenic and food spoilage microorganisms (e.g., Escherichia, Shigella, Klebsiella, etc.) were also present, but the study demonstrated the safety potential of the Sesotho fermentation process, as these microbial groups decline throughout Sesotho production. The functional profiles of the different brewing steps showed that the process is dominated by chemoheterotrophic and fermentative metabolisms. This study reveals, for the first time, the complex microbial dynamics that occur during Sesotho production.
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Affiliation(s)
- Errol D. Cason
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
- Department of Animal, Wildlife, and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Bokang J. Mahlomaholo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Matšepo M. Taole
- Department of Biology, National University of Lesotho, Maseru, Lesotho
| | - George Ooko Abong
- Department of Food Science, Nutrition and Technology, University of Nairobi, Nairobi, Kenya
| | - Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Olga de Smidt
- Centre for Applied Food Sustainability and Biotechnology (CAFSaB), Central University of Technology, Bloemfontein, South Africa
| | - Marcele Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Laurinda Steyn
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Angel Valverde
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Bennie Viljoen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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