scholarly journals Biological Trace Information Extracted from Bioaerosols Using NGS Analysis

2021 ◽  
Vol 37 ◽  
pp. e37090
Author(s):  
Panyapon Pumkaeo ◽  
Wenhao Lu ◽  
Youki Endou ◽  
Tomofumi Mizuno ◽  
Junko Takahashi ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Fungal Species ◽  
Biological Information ◽  
Plant Identification ◽  
Its1 Region ◽  
Air Sampler ◽  
Plant Chloroplast ◽  
Animal Detection ◽  
Generation Sequencing ◽  
Diverse Plant

Bioaerosols are atmospheric particles with a biological trace, such as viruses, bacteria, fungi, and plant material such as pollen and plant debris. In this study, we analyzed the biological information in bioaerosols using next generation sequencing of the trace DNA. The samples were collected using an Andersen air sampler and separated into two groups according to particulate matter (PM) size: small (PM2.5) and large (PM10). Amplification and sequencing of the bacterial 16S rDNA gene, prokaryotic internal transcribed spacer 1 (ITS1) region and DNA sequence of a plant chloroplast gene (rbcL) were carried out using several sets of specific primers targeting animal and plant sequences. Lots of bacterial information was detected from the bioaerosols. The most abundant bacteria in several samples were of the Actinobacteria (class), Alphaproteobacteria, Bacilli, and Clostridia. For the animal detection using internal transcribed spacer 1, only uncultured fungi were detected in more than half of the hits, with a high number of Cladosporium sp. in the samples. For the plant identification, the ITS1 information only matched fungal species. However, targeting of the rbcL region revealed diverse plant information, such as Medicago papillosa. In conclusion, traces of bacteria, fungi, and plants could be detected in the bioaerosols, but not of animals using our primers.

Characterizing the Microbiome of the Contracted Breast Capsule Using Next Generation Sequencing

2020 ◽  
Author(s):  
Jonathan Cook ◽  
Casey J Holmes ◽  
Roger Wixtrom ◽  
Martin I Newman ◽  
Jason N Pozner
Keyword(s):  
Next Generation Sequencing ◽  
Capsular Contracture ◽  
Bacterial Species ◽  
Fungal Species ◽  
Augmentation Mammoplasty ◽  
Next Generation ◽  
Level Of Evidence ◽  
Cutibacterium Acnes ◽  
Microbial Dna ◽  
Generation Sequencing

Abstract Background Recent work suggests that bacterial biofilms play a role in capsular contracture (CC). However, traditional culture techniques provide only a limited understanding of the bacterial communities present within the contracted breast. Next generation sequencing (NGS) represents an evolution of polymerase chain reaction technology that can sequence all DNA present in a given sample. Objectives The aim of this study was to utilize NGS to characterize the bacterial microbiome of the capsule in patients with CC following cosmetic breast augmentation. Methods We evaluated 32 consecutive patients with Baker grade III or IV CC following augmentation mammoplasty. Specimens were obtained from all contracted breasts (n = 53) during capsulectomy. Tissue specimens from contracted capsules as well as intraoperative swabs of the breast capsule and implant surfaces were obtained. Samples were sent to MicroGenDX Laboratories (Lubbock, TX) for NGS. Results Specimens collected from 18 of 32 patients (56%) revealed the presence of microbial DNA. The total number of positive samples was 22 of 53 (42%). Sequencing identified a total of 120 unique bacterial species and 6 unique fungal species. Specimens with microbial DNA yielded a mean [standard deviation] of 8.27 [4.8] microbial species per patient. The most frequently isolated species were Escherichia coli (25% of all isolates), Diaphorobacter nitroreducens (12%), Cutibacterium acnes (12%), Staphylococcus epidermidis (11%), fungal species (7%), and Staphylococcus aureus (6%). Conclusions NGS enables characterization of the bacterial ecosystem surrounding breast implants in unprecedented detail. This is a critical step towards understanding the role this microbiome plays in the development of CC. Level of Evidence: 4

Genetic Diversity and Origin of Siam Weed (Chromolaena odorata) in Australia

1998 ◽  
Vol 12 (1) ◽  
pp. 27-31 ◽  
Author(s):  
Leon J. Scott ◽  
Corinna L. Lange ◽  
Glenn C. Graham ◽  
David K. Yeates
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Southern Brazil ◽  
Chromolaena Odorata ◽  
Base Pairs ◽  
Its1 Sequence ◽  
Its1 Region ◽  
Native And Introduced Ranges ◽  
The U.S

Asynchronous flowering was noted in a recently discovered infestation of siam weed in north Queensland. This may indicate some genetic diversity in the infestation, increasing concerns about the origin of the infestation. Internal transcribed spacer 1 (ITS1) sequence data were obtained for siam weed individuals from north Queensland, Indonesia, Thailand, South Africa, Ivory Coast, Brazil, Colombia, and the U.S. The ITS1 region is 258 base pairs long, and the populations that flower at different times in north Queensland differ by four base substitutions. The genotype common in north Queensland is also reported throughout the native and introduced ranges. The other genotype is reported only in north Queensland and southern Brazil. These data, in conjunction with prior investigations into possible origins, indicate that Brazil is the most likely source of the infestation in Australia.

scholarly journals Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location, and Interaction with Bacteria

2019 ◽  
Vol 85 (9) ◽  
Author(s):  
Alba Boix-Amorós ◽  
Fernando Puente-Sánchez ◽  
Elloise du Toit ◽  
Kaisa M. Linderborg ◽  
Yumei Zhang ◽  
...  
Keyword(s):  
Breast Milk ◽  
Potential Role ◽  
Mode Of Delivery ◽  
Geographical Location ◽  
Geographic Location ◽  
Fungal Species ◽  
Human Breast Milk ◽  
Human Breast ◽  
Its1 Region ◽  
Milk Samples

ABSTRACTRecent studies report the presence of fungal species in breast milk of healthy mothers, suggesting a potential role in infant mycobiome development. In the present work, we aimed to determine whether the healthy human breast milk mycobiota is influenced by geographical location and mode of delivery, as well as to investigate its interaction with bacterial profiles in the same samples. A total of 80 mature breast milk samples from 4 different countries were analyzed by Illumina sequencing of the internal transcribed spacer 1 (ITS1) region, joining the 18S and 5.8S regions of the fungal rRNA region. Basidiomycota and Ascomycota were found to be the dominant phyla, withMalasseziaandDavidiellabeing the most prevalent genera across countries. A core formed byMalassezia, Davidiella, Sistotrema, andPenicilliumwas shared in the milk samples from the different origins, although specific shifts in mycobiome composition were associated with geographic location and delivery mode. The presence of fungi in the breast milk samples was further confirmed by culture and isolate characterization, and fungal loads were estimated by quantitative PCR (qPCR) targeting the fungal ITS1 region. Cooccurrence network analysis of bacteria and fungi showed complex interactions that were influenced by geographical location, mode of delivery, maternal age, and pregestational body mass index. The presence of a breast milk mycobiome was confirmed in all samples analyzed, regardless of the geographic origin.IMPORTANCEDuring recent years, human breast milk has been documented as a potential source of bacteria for the newborn. Recently, we have reported the presence of fungi in breast milk from healthy mothers. It is well known that environmental and perinatal factors can affect milk bacteria; however, the impact on milk fungi is still unknown. The current report describes fungal communities (mycobiota) in breast milk samples across different geographic locations and the influence of the mode of delivery. We also provide novel insights on bacterium-fungus interactions, taking into account environmental and perinatal factors. We identified a core of four genera shared across locations, consisting ofMalassezia, Davidiella, Sistotrema, andPenicillium, which have been reported to be present in the infant gut. Our data confirm the presence of fungi in breast milk across continents and support the potential role of breast milk in the initial seeding of fungal species in the infant gut.

What Else Is in Salviae officinalis folium? Comprehensive Species Identification of Plant Raw Material by DNA Metabarcoding

Planta Medica ◽  
2017 ◽  
Vol 84 (06/07) ◽  
pp. 428-433 ◽  
Author(s):  
Corinna Schmiderer ◽  
Brigitte Lukas ◽  
Joana Ruzicka ◽  
Johannes Novak
Keyword(s):  
Next Generation Sequencing ◽  
Dna Barcoding ◽  
Species Identification ◽  
Internal Transcribed Spacer ◽  
Raw Material ◽  
Next Generation ◽  
Additional Species ◽  
Internal Transcribed Spacer 2 ◽  
Dna Metabarcoding ◽  
Generation Sequencing

AbstractQuality control of drugs consists of identifying the raw material to avoid unwanted admixtures or exchange of material as well as looking for abiotic and biotic contaminations. So far, identity and microbial contamination are analyzed by separate processes and separate methods. Species identification by their DNA (“DNA barcoding”) has the potential to supplement existing methods of identification. The introduction of next-generation sequencing methods offers completely new approaches like the identification of whole communities in one analysis, termed “DNA metabarcoding”. Here we present a next-generation sequencing assessment to identify plants and fungi of two commercial sage samples (Salvia officinalis) using the standard DNA barcoding region “internal transcribed spacer” consisting of internal transcribed spacer 1 and internal transcribed spacer 2, respectively. The main species in both samples was identified as S. officinalis. The spectrum of accompanying plant and fungal species, however, was completely different between the samples. Additionally, the composition between internal transcribed spacer 1 and internal transcribed spacer 2 within the samples was different and demonstrated the influence of primer selection and therefore the need for harmonization. This next-generation sequencing approach does not result in quantitative species composition but gives deeper insight into the composition of additional species. Therefore, it would allow for a better knowledge-based risk assessment than any other method available. However, the method is only economically feasible in routine analysis if a high sample throughput can be guaranteed.

scholarly journals An Emerging Pathogen from Rotted Chestnut in China: Gnomoniopsis daii sp. nov.

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1016 ◽  
Author(s):  
Ning Jiang ◽  
Chengming Tian
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Brown Rot ◽  
Fungal Species ◽  
Fruit Rot ◽  
Economic Viability ◽  
Emerging Pathogen ◽  
Morphological Comparison ◽  
Sweet Chestnut ◽  
Rot Disease

Nut quality is fundamental to the economic viability of the Chinese sweet chestnut industry, but fruit rot disease significantly reduces this quality. In this study, we investigated chestnut rot in Anhui and Hubei provinces in China. Typical brown rot symptoms were observed, affecting nuts from different plantations. Isolates were obtained from symptomatic tissues of rotted fruits that were identified based on morphological comparison and phylogenetic analyses of partial internal transcribed spacer (ITS), and tef1 and tub2 gene sequences. The inoculation results showed that the tested fungal species is pathogenic to chestnut fruits. Hence, a new and severe pathogen that causes Chinese sweet chestnut brown rot, Gnomoniopsis daii sp. nov., is introduced herein.

Diaporthe sinensis, a new fungus from Amaranthus sp. in China 

Phytotaxa ◽  
2019 ◽  
Vol 425 (5) ◽  
pp. 259-268
Author(s):  
XIAO-XIAO FENG ◽  
JIA-JIE CHEN ◽  
GUO-RONG WANG ◽  
TING-TING CAO ◽  
YONG-LI ZHENG ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Fungal Species ◽  
Translation Elongation Factor ◽  
Translation Elongation ◽  
Stems And Leaves ◽  
Elongation Factor 1 ◽  
Β Tubulin

During an exploration of plant pathogens in vegetables occuring in Zhejiang province, China, a novel fungal species, was found. Three strains ZJUP0033-4, ZJUP0038-3 and ZJUP0132 were isolated from black round lesions in the stems and leaves of Amaranthus sp. Phylogenetic analyses based on sequences from four genes including rDNA internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α), histone (HIS) and β-tubulin (TUB) indicated that D. sinensis clustered in a distinct clade closely related to D. neoarctii, D. angelicae, D. subordinaria, D. arctii, D. cuppatea, D. lusitanicae, D. novem, D. infecunda, D. ganjae and D. manihotia. Morphologically, D. sinensis is distinguished by brown, scattered, globose pycnidia and ellipsoid alpha conidia with bi- to multiguttulate.

scholarly journals Conservation of griseofulvin genes in the gsf gene cluster among fungal genomes

2021 ◽  
Author(s):  
Parisa Aris ◽  
Lihong Yan ◽  
Yulong Wei ◽  
Ying Chang ◽  
Bihong Shi ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Fungal Species ◽  
Antifungal Compound ◽  
Biosynthetic Gene ◽  
Polyketide Biosynthesis ◽  
Third Generation Sequencing ◽  
Penicillium Griseofulvum ◽  
Fungal Genomes ◽  
Generation Sequencing

Abstract The polyketide griseofulvin is a natural antifungal compound and research in griseofulvin has been key in establishing our current understanding of polyketide biosynthesis. Nevertheless, the griseofulvin gsf biosynthetic gene cluster (BGC) remains poorly understood in most fungal species, including Penicillium griseofulvum where griseofulvin was first isolated. To elucidate essential genes involved in griseofulvin biosynthesis, we performed third-generation sequencing to obtain the genome of Penicillium griseofulvum strain D-756. Furthermore, we gathered publicly available genome of 11 other fungal species in which gsf gene cluster was identified. In a comparative genome analysis, we annotated and compared the gsf BGC of all 12 fungal genomes. Our findings show no gene rearrangements at the gsf BGC. Furthermore, seven gsf genes are conserved by most genomes surveyed whereas the remaining six were poorly conserved. This study provides new insights into differences between gsf BGC and suggests that seven gsf genes are essential in griseofulvin production.

scholarly journals Telomere Length De Novo Assembly of all 7 Chromosomes and Mitogenome Sequencing of the Model Entomopathogenic Fungus, Metarhizium Brunneum, by Means of a Novel Assembly Pipeline

2020 ◽  
Author(s):  
Zack Saud ◽  
Alexandra M. Kortsinoglou ◽  
Vassili N. Kouvelis ◽  
Tariq M. Butt
Keyword(s):  
Entomopathogenic Fungus ◽  
De Novo ◽  
Gene Prediction ◽  
Fungal Species ◽  
Orthologous Protein ◽  
Metarhizium Brunneum ◽  
Sequencing Technologies ◽  
Protein Clusters ◽  
Assembly Pipeline ◽  
Generation Sequencing

Abstract More accurate and complete reference genomes have improved understanding of gene function, biology, and evolutionary mechanisms. Hybrid genome assembly approaches leverage benefits of both long, relatively error-prone reads from third-generation sequencing technologies and short, accurate reads from second-generation sequencing technologies, to produce more accurate and contiguous de novo genome assemblies in comparison to using either technology independently. In this study, we present a novel hybrid assembly pipeline that allowed for both mitogenome de novo assembly and telomere length de novo assembly of all 7 chromosomes of the model entomopathogenic fungus, Metarhizium brunneum. The improved assembly allowed for better ab initio gene prediction and a more BUSCO complete proteome set has been generated in comparison to the eight current NCBI reference Metarhizium spp. genomes. Remarkably, we note that including the mitogenome in ab initio gene prediction training improved overall gene prediction. The assembly was further validated by comparing contig assembly agreement across various assemblers, assessing the assembly performance of each tool. Genomic synteny and orthologous protein clusters were compared between Metarhizium brunneum and three other Hypocreales species with complete genomes, identifying core proteins, and listing orthologous protein clusters shared uniquely between the two entomopathogenic fungal species, so as to further facilitate the understanding of molecular mechanisms underpinning fungal-insect pathogenesis. The novel assembly pipeline may be used for other haploid fungal species, facilitating the need to produce high-quality reference fungal genomes, leading to better understanding of fungal genomic evolution, chromosome structuring and gene regulation.

scholarly journals Description of Lepiotaceous Fungal Species of the Genera Chlorophyllum, Clarkeinda, Macrolepiota, Pseudolepiota, and Xanthagaricus, from Laos and Thailand

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 666
Author(s):  
Phongeun Sysouphanthong ◽  
Naritsada Thongklang ◽  
Jian-Kui Liu ◽  
Else C. Vellinga
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Fungal Species ◽  
Ongoing Research ◽  
Line Drawings ◽  
Dna And Rna ◽  
First Time

In our ongoing research on lepiotaceous taxa (Agaricaceae s.l.) in Laos and northern Thailand, we focus here on Chlorophyllum, Clarkeinda, Macrolepiota, Pseudolepiota, and Xanthagaricus. Collections were obtained from various habitats, including agricultural habitats, grasslands, and rainforests. A total of 12 taxa were examined and investigated. Of these 12, two are new for science; viz. Xanthagaricus purpureosquamulosus with brownish-grey to violet-brown squamules on a pale-violet to violet background; it shares the pileus color with X. caeruleus and X. ianthinus, but differs in other characters; and Macrolepiota excelsa, rather similar to M. procera but related toM. detersa. Two species, Pseudolepiota zangmui and Xanthagaricus necopinatus are recorded for the first time in Thailand. Four species of Chlorophyllum and a total of four species of Macrolepiota were found, viz., C. demangei and C. hortense with white basidiospores, C. molybdites and C. globosum with green basidiospores, M. detersa, M. dolichaula, the new M. excelsa, and M. velosa. Another rather common striking species is Clarkeinda trachodes, with yellow-green basidiospores. Each species is described in detail, with color photographs and line drawings. Phylogenetic analyses based on internal transcribed spacer (nrITS) region, the large subunit nuclear ribosomal (nrLSU) DNA and RNA polymerase II second largest subunit (rpb2) genes provide evidence for the placement of the species covered.

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