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Paskey AC, Schully KL, Voegtly LJ, Arnold CE, Cer RZ, Frey KG, Blair PW, Clark DV, Ge H, Richards AL, Farris CM, Bishop-Lilly KA. A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens. Front Microbiol 2024; 15:1387208. [PMID: 38659991 PMCID: PMC11039911 DOI: 10.3389/fmicb.2024.1387208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Paul W. Blair
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Danielle V. Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Allen L. Richards
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Christina M. Farris
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
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Schroeder JW, Freddolino PL. Enricherator: A Bayesian Method for Inferring Regularized Genome-wide Enrichments from Sequencing Count Data. J Mol Biol 2024:168567. [PMID: 38583516 DOI: 10.1016/j.jmb.2024.168567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
A pervasive question in biological research studying gene regulation, chromatin structure, or genomics is where, and to what extent, does a signal of interest arise genome-wide? This question is addressed using a variety of methods relying on high-throughput sequencing data as their final output, including ChIP-seq for protein-DNA interactions,1 GapR-seq for measuring supercoiling,2 and HBD-seq or DRIP-seq for R-loop positioning.3,4 Current computational methods to calculate genome-wide enrichment of the signal of interest usually do not properly handle the count-based nature of sequencing data, they often do not make use of the local correlation structure of sequencing data, and they do not apply any regularization of enrichment estimates. This can result in unrealistic estimates of the true underlying biological enrichment of interest, unrealistically low estimates of confidence in point estimates of enrichment (or no estimates of confidence at all), unrealistic gyrations in enrichment estimates at very close (<10 bp) genomic loci due to noise inherent in sequencing data, and in a multiple-hypothesis testing problem during interpretation of genome-wide enrichment estimates. We developed a tool called Enricherator to infer genome-wide enrichments from sequencing count data. Enricherator uses the variational Bayes algorithm to fit a generalized linear model to sequencing count data and to sample from the approximate posterior distribution of enrichment estimates (https://github.com/jwschroeder3/enricherator). Enrichments inferred by Enricherator more precisely identify known binding sites in cases where low coverage between binding sites leads to false-positive peak calls in these noisy regions of the genome; these benefits extend to published datasets.
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Affiliation(s)
- Jeremy W Schroeder
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - P Lydia Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
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Fu Y, Qu Z, Wang Y, Sun P, Jiao N, Xu D. Biogeographical and biodiversity patterns of planktonic microeukaryotes along the tropical western to eastern Pacific Ocean transect revealed by metabarcoding. Microbiol Spectr 2024; 12:e0242423. [PMID: 38488393 DOI: 10.1128/spectrum.02424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
Microeukaryotic plankton (0.2-200 µm), which are morphologically and genetically highly diverse, play a crucial role in ocean productivity and carbon consumption. The Pacific Ocean (PO), one of the world's largest oligotrophic regions, remains largely unexplored in terms of the biogeography and biodiversity of microeukaryotes based on large-scale sampling. We investigated the horizontal distribution of microeukaryotes along a 16,000 km transect from the west to the east of the PO. The alpha diversity indices showed a distinct decreasing trend from west to east, which was highly correlated with water temperature. The microeukaryotic community, which was clustered into the western, central, and eastern PO groups, displayed a significant distance-decay relationship. Syndiniales, a lineage of parasitic dinoflagellates, was ubiquitously distributed along the transect and dominated the community in terms of both sequence and zero-radius operational taxonomic unit (ZOTU) proportions. The prevailing dominance of Syndiniales-affiliated ZOTUs and their close associations with dinoflagellates, diatoms, and radiolarians, as revealed by SparCC correlation analysis, suggested that parasitism may be an important trophic strategy in the surface waters of the PO. Geographical distance and temperature were the most important environmental factors that significantly correlated with community structure. Overall, our study sheds more light on the distribution pattern of both alpha and beta diversities of microeukaryotic communities and highlighted the importance of parasitisms by Syndiniales across the tropical PO.IMPORTANCEUnderstanding the biogeographical and biodiversity patterns of microeukaryotic communities is essential to comprehending their roles in biogeochemical cycling. In this study, planktonic microeukaryotes were collected along a west-to-east Pacific Ocean transect (ca. 16,000 km). Our study revealed that the alpha diversity indices were highly correlated with water temperature, and the microeukaryotic communities displayed a distinct geographical distance-driven pattern. The predominance of the parasitic dinoflagellate lineage Syndiniales and their close relationship with other microeukaryotic groups suggest that parasitism may be a crucial survival strategy for microeukaryotes in the surface waters of the Pacific Ocean. Our findings expand our understanding of the biodiversity and biogeographical pattern of microeukaryotes and highlight the significance of parasitic Syndiniales in the surface ocean.
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Affiliation(s)
- Yingjun Fu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Zhishuai Qu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Ying Wang
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of Ministry of Education for Coastal and Wetland Ecosystems, Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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Kumar V, Ameen F, Verma P. Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach. Front Microbiol 2024; 15:1350164. [PMID: 38529176 PMCID: PMC10961449 DOI: 10.3389/fmicb.2024.1350164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.
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Affiliation(s)
- Vineet Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Fan L, Guan G, Zhao J, Li D, Yu X, Shentu X. Comparative analysis of the diversity of symbionts in fat body of long- and short-winged brown planthoppers. Arch Insect Biochem Physiol 2024; 115:e22096. [PMID: 38500448 DOI: 10.1002/arch.22096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
The microbial community structure plays an important role in the internal environment of brown planthopper (BPH), Nilaparvata lugens (Hemiptera: Delphacidae), which is an indispensable part to reflect the internal environment of BPH. Wing dimorphism is a strategy for balancing flight and reproduction of insects. Here, quantitative fluorescence PCR was used to analyse the number and changes of the symbionts in the fat body of long- and short-winged BPHs at different developmental stages. A metagenomic library was constructed based on the 16 S rRNA sequence and internal transcribed spacer sequence for high-throughput sequencing, to analyze the community structure and population number of the symbionts of long- and short-winged BPHs, and to make functional prediction. This study enriches the connotation of BPH symbionts, and laid a theoretical foundation for the subsequent study of BPH-symbionts interaction and the function of symbionts in the host.
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Affiliation(s)
- Linlin Fan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Guangxiang Guan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Jingjing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Danting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China Jiliang University, Hangzhou, China
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Wu Z, Xu M, He W, Li X, Qiu C, Zhang J. Unraveling the Physicochemical Properties and Bacterial Communities in Rabbit Meat during Chilled Storage. Foods 2024; 13:623. [PMID: 38397599 PMCID: PMC10887707 DOI: 10.3390/foods13040623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
The freshness and bacterial communities of fresh and salted rabbit meat during 8 days of refrigerated storage at 4 °C were evaluated. The results showed that the addition of 2% salt significantly changed the color of meat, of which the lightness (L*), redness (a*), and yellowness (b*) were lower than that of fresh meat over time. The pH of all samples increased during storage, and meat with salt addition had lower values in comparison to fresh samples over time. The total volatile base nitrogen (TVB-N) concentration increased rapidly in salt-treated meat but was significantly (p < 0.05) lower than that in meat without salt added before 6 days. Over time, the content of thiobarbituric acid reactive substances (TBARS) showed a progressive trend, but a rapid increase occurred in salted meat. High-throughput sequencing showed that the microflora of each sample had a positive trend in alpha diversity and a negative trend in beta diversity. Bacterial taxonomic analysis indicated that the initial microbial flora for chilled rabbit meat was dominated by Shigaella, Bacteroides, and Lactococcus, and the population of Brochothrix and Psychrobacter increased over time and became the dominant spoilage bacterium. In particular, the addition of salt significantly reduced the abundance of Psychrobacter and Brochothrix. These findings might provide valuable information regarding the quality monitoring of rabbit meat during chilled storage.
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Affiliation(s)
- Zhoulin Wu
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
- Development and Research Center of Sichuan Cuisine, Sichuan Tourism University, Chengdu 610100, China
| | - Maoqin Xu
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
| | - Wei He
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
| | - Xiaoyu Li
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
| | - Chaoqing Qiu
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
| | - Jiamin Zhang
- Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (Z.W.); (M.X.); (W.H.); (X.L.); (C.Q.)
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Borewicz K, Brück WM. Supplemented Infant Formula and Human Breast Milk Show Similar Patterns in Modulating Infant Microbiota Composition and Function In Vitro. Int J Mol Sci 2024; 25:1806. [PMID: 38339084 PMCID: PMC10855883 DOI: 10.3390/ijms25031806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The gut microbiota of healthy breastfed infants is often dominated by bifidobacteria. In an effort to mimic the microbiota of breastfed infants, modern formulas are fortified with bioactive and bifidogenic ingredients. These ingredients promote the optimal health and development of infants as well as the development of the infant microbiota. Here, we used INFOGEST and an in vitro batch fermentation model to investigate the gut health-promoting effects of a commercial infant formula supplemented with a blend containing docosahexaenoic acid (DHA) (20 mg/100 kcal), polydextrose and galactooligosaccharides (PDX/GOS) (4 g/L, 1:1 ratio), milk fat globule membrane (MFGM) (5 g/L), lactoferrin (0.6 g/L), and Bifidobacterium animalis subsp. lactis, BB-12 (BB-12) (106 CFU/g). Using fecal inoculates from three healthy infants, we assessed microbiota changes, the bifidogenic effect, and the short-chain fatty acid (SCFA) production of the supplemented test formula and compared those with data obtained from an unsupplemented base formula and from the breast milk control. Our results show that even after INFOGEST digestion of the formula, the supplemented formula can still maintain its bioactivity and modulate infants' microbiota composition, promote faster bifidobacterial growth, and stimulate production of SCFAs. Thus, it may be concluded that the test formula containing a bioactive blend promotes infant gut microbiota and SCFA profile to something similar, but not identical to those of breastfed infants.
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Affiliation(s)
- Klaudyna Borewicz
- Mead Johnson B.V., Middenkampweg 2, 6545 CJ Nijmegen, The Netherlands;
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion, Switzerland
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. Sci China Life Sci 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Lanzavecchia G, Frascarelli G, Rocchetti L, Bellucci E, Bitocchi E, Di Vittori V, Sillo F, Ferraris I, Carta G, Delledonne M, Nanni L, Papa R. Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System. Int J Mol Sci 2024; 25:1288. [PMID: 38279288 PMCID: PMC10815965 DOI: 10.3390/ijms25021288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/23/2023] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.
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Affiliation(s)
- Giovanna Lanzavecchia
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Giulia Frascarelli
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Lorenzo Rocchetti
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Valerio Di Vittori
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Fabiano Sillo
- National Research Council of Italy, Institute for Sustainable Plant, Strada delle Cacce 73, 10135 Torino, Italy;
| | - Irene Ferraris
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Giada Carta
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Massimo Delledonne
- Department of Biotechnologies, Strada le Grazie 15, 37134 Verona, Italy; (I.F.); (G.C.); (M.D.)
| | - Laura Nanni
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy; (G.L.); (G.F.); (L.R.); (E.B.); (E.B.); (V.D.V.)
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10
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Goldmann K. Editorial: Fungal diversity of forests: phylogeny, taxonomy and pathology. Front Microbiol 2024; 14:1353548. [PMID: 38282735 PMCID: PMC10822687 DOI: 10.3389/fmicb.2023.1353548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024] Open
Affiliation(s)
- Kezia Goldmann
- Department Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
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11
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Cai M, Lin L, Jiang F, Peng Y, Li S, Chen L, Lin Y. Gut microbiota changes in patients with hypertension: A systematic review and meta-analysis. J Clin Hypertens (Greenwich) 2023; 25:1053-1068. [PMID: 37853925 PMCID: PMC10710550 DOI: 10.1111/jch.14722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 10/20/2023]
Abstract
Hypertension is a major public health issue worldwide. The imbalance of gut microbiota is thought to play an important role in the pathogenesis of hypertension. The authors conducted the systematic review and meta-analysis to clarify the relationship between gut microbiota and hypertension through conducting an electronic search in six databases. Our meta-analysis included 19 studies and the results showed that compared with healthy controls, Shannon significantly decreased in hypertension [SMD = -0.13, 95%CI (-0.22, -0.04), p = .007]; however, Simpson [SMD = -0.01, 95%CI (-0.14, 0.12), p = .87], ACE [SMD = 0.18, 95%CI (-0.06, 0.43), p = .14], and Chao1 [SMD = 0.11, 95%CI (-0.01, 0.23), p = .08] did not differ significantly between hypertension and healthy controls. The F/B ratio significantly increased in hypertension [SMD = 0.84, 95%CI (0.10, 1.58), p = .03]. In addition, Shannon index was negatively correlated with hypertension [r = -0.12, 95%CI (-0.19, -0.05)], but had no significant correlation with SBP [r = 0.10, 95%CI (-0.19, 0.37)] and DBP [r = -0.39, 95%CI (-0.73, 0.12)]. At the phylum level, the relative abundance of Firmicutes [SMD = -0.01, 95%CI (-0.37, 0.34), p = .94], Bacteroidetes [SMD = -0.15, 95%CI (-0.44, 0.14), p = .30], Proteobacteria [SMD = 0.25, 95%CI (-0.01, 0.51), p = .06], and Actinobacteria [SMD = 0.21, 95%CI (-0.11, 0.53), p = .21] did not differ significantly between hypertension and healthy controls. At the genus level, compared with healthy controls, the relative abundance of Faecalibacterium decreased significantly [SMD = -0.16, 95%CI (-0.28, -0.04), p = .01], while the Streptococcus [SMD = 0.20, 95%CI (0.08, 0.32), p = .001] and Enterococcus [SMD = 0.20, 95%CI (0.08, 0.33), p = .002] significantly increased in hypertension. Available evidence suggests that hypertensive patients may have an imbalance of gut microbiota. However, it still needs further validation by large sample size studies of high quality.
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Affiliation(s)
- Meiling Cai
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
- Fujian Provincial Special Reserve Talents LaboratoryFujian Medical University Union HospitalFuzhouChina
| | - Lingyu Lin
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
| | - Fei Jiang
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
- Fujian Provincial Special Reserve Talents LaboratoryFujian Medical University Union HospitalFuzhouChina
| | - Yanchun Peng
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
| | - Sailan Li
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
| | - Liangwan Chen
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
- Fujian Provincial Special Reserve Talents LaboratoryFujian Medical University Union HospitalFuzhouChina
| | - Yanjuan Lin
- Department of NursingFujian Medical University Union HospitalFuzhouChina
- Department of Cardiovascular SurgeryFujian Medical University Union HospitalFuzhouChina
- Fujian Provincial Special Reserve Talents LaboratoryFujian Medical University Union HospitalFuzhouChina
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12
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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Pastoret C, Wahl C, Castet S, Nedelec F, Pontis A, Bayart S, Fest T, Guillet B. Five new F10 variants in hereditary factor x deficiency detected by high-throughput sequencing. Haemophilia 2023; 29:1565-1572. [PMID: 37842794 DOI: 10.1111/hae.14888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/17/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION Factor X deficiency is a rare inherited bleeding disorder. To date, 181 variants are reported in the recently updated F10-gene variant database. AIM This study aimed to describe new F10 variants. METHOD The F10 gene was analysed in 16 consecutive families with FX deficiency by a targeted high-throughput sequencing approach, including F10, F9, F8 genes, and 78 genes dedicated to haematological malignancies. RESULTS We identified 19 variants (17 missense, one nonsense and one frameshift) and two copy number variations. Two patients presenting a combined FVII-FX deficiency showed a loss of one F10 gene copy (del13q34) associated with a missense variant on the remaining allele, leading to a FX:C significantly lower than the FVII:C level and explaining their unusual bleeding history. We reported five novel variants. Three missense variants (p.Glu22Val affecting the signal peptide cleavage site, p.Cys342Tyr removing the disulphide bond between the FX heavy and light chains, and p.Val385Met located in FX peptidase S1 domain) were detected at compound heterozygosis status in three patients with severe bleeding symptoms and FX:C level below 10 IU/dL. Two truncating variants p.Tyr279* and p.Thr434Aspfs*13 leading to an altered FX protein were found at heterozygous state in two patients with mild bleeding history. CONCLUSION This study showed the feasibility and the interest of high-throughput sequencing approach for rare bleeding disorders, enabling the report of F10 gene screening in a 3-weeks delay, suitable for clinical use. The description of five new variants may contribute to a better understanding of the phenotype-genotype correlation in FX deficiency.
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Affiliation(s)
- Cédric Pastoret
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
| | - Clémentine Wahl
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
| | | | - Fabienne Nedelec
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
- CRC-MHC, CHU de Rennes, Rennes, France
| | - Adeline Pontis
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
| | - Sophie Bayart
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
- CRC-MHC, CHU de Rennes, Rennes, France
| | - Thierry Fest
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
| | - Benoît Guillet
- Laboratoire d'Hématologie, Pôle de Biologie, CHU de Rennes, Rennes, France
- CRC-MHC, CHU de Rennes, Rennes, France
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
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Chen L, Zhou Z, Wang SQ. Process of Forensic Medicine in DNA Identification of Aged Human Remains. Fa Yi Xue Za Zhi 2023; 39:478-486. [PMID: 38006268 DOI: 10.12116/j.issn.1004-5619.2021.511209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
Skeleton and teeth are important biological samples. Due to their special structure and strong ability to resist degradation, they are ideal biological materials to retain DNA under natural condition. In many cases, such as historical figure identification, aged skeleton and teeth are usually the only biological samples. However, their DNA is in a state of trace, damage and degradation to different degrees, which requires special experimental treatment to achieve identification. This paper reviews the sample selection, DNA extraction, DNA enrichment and analysis approaches based on relevant research reports in recent years, aiming to promote the further development and improvement of the aged skeleton and teeth identification system.
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Affiliation(s)
- Lu Chen
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
| | - Zhe Zhou
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
| | - Sheng-Qi Wang
- Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China
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15
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Jia PY, Wang X, Hua YT, Jiang ZX. [Effects of Different Biochar and Effective Microorganism Agent Improvement Approaches on the Nutrient Release Characteristics and Potential of Compost]. Huan Jing Ke Xue 2023; 44:5025-5035. [PMID: 37699820 DOI: 10.13227/j.hjkx.202210085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The nutrient release characteristics of four types of composts, pure municipal sewage sludge compost, corn straw biochar (CSB) improved compost, effective microorganism agent (EM) improved compost, and CSB+EM improved compost, in coastal wetland soil were examined through a soil incubation experiment. The effects of different composts on the spectral characteristics of soil dissolved organic matter (DOM) and microbial community were also investigated. The results demonstrated that the compost additions could significantly reduce soil pH, while increasing soil electrical conductivity and contents of plant available nutrients (e.g., dissolved organic carbon, NH4+-N, NO3--N, available phosphorus, and available potassium). By comparing the nutrient release potential among the improved composts, the CSB+EM-improved compost (CSB+EM-C) evidently had the highest nutrient release potential. Furthermore, the DOM in CSB+EM-C amended soil exhibited a higher humification degree than that of the other composts. The high-throughput sequencing results indicated that the compost additions increased the relative abundances of dominant bacteria at the phylum level, such as the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. CSB+EM-C exhibited a greater potential to improve the relative abundance of these dominant bacteria phyla than other improved composts. Overall, among all the improvement approaches, the combined use of CSB and EM agent was the optimal composting strategy owing to its highest potentials of nutrient supply and soil quality improvement. The present findings can provide a solid scientific theoretical basis for establishing an effective technology strategy involving the combination of municipal sewage sludge utilization and degraded coastal wetland soil remediation.
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Affiliation(s)
- Pei-Yin Jia
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
- Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
| | - Xin Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
- Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
| | - Yu-Ting Hua
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
- Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
| | - Zhi-Xiang Jiang
- College of Environmental Science and Engineering, Qingdao University, Qingdao 266071, China
- Carbon Neutrality and Eco-Environmental Technology Innovation Center of Qingdao, Qingdao 266071, China
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16
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Lu M, Lu F, Liao C, Guo Y, Mao C, Lai Y, Chen X, Chen W. High throughput miRNA sequencing and bioinformatics analysis identify the mesenchymal cell proliferation and apoptosis related miRNAs during fetal mice palate development. J Gene Med 2023; 25:e3531. [PMID: 37317697 DOI: 10.1002/jgm.3531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Palatogenesis requires a precise spatiotemporal regulation of gene expression. Recent studies indicate that microRNAs (miRNAs) are key factors in normal palatogenesis. The present study aimed to explain the regulatory mechanisms of miRNAs during palate development. METHODS Pregnant ICR mice were choose at embryonic day 10.5 (E10.5). Hemotoxylin and eosin (H&E) staining was used to observe the morphological changes during the development of palatal process at embryonic day (E)13.5, E14.0, E14.5, E15.0 and E15.5. The fetal palatal tissues were collected at E13.5, E14.0, E14.5 and E15.0 to explore miRNA expression and function by high throughput sequencing and bioinformatic analysis. Mfuzz cluster analysis was used to look for miRNAs related to the fetal mice palate formation. The target genes of miRNAs were predicted by miRWalk. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed base on target genes. The mesenchymal cell proliferation and apoptosis related miRNAs-genes networks were predicted and constructed using miRWalk and Cytoscape software. The expression of mesenchymal cell proliferation and apoptosis related miRNAs at the E13.5, E14.0, E14.5, and E15.0 was detected by a quantitative real-time PCR (RT-qPCR) assay. RESULTS H&E staining found that the palatal process grows vertically along the sides of the tongue at E13.5, the position of the tongue begins to descend and the bilateral palatal processes rise above the tongue at E14.0, the palatal process grows horizontally at E14.5, there is palatal contact fusion at E15.0, and the palatal suture disappeared at E15.5. Nine clusters of miRNA expression changes were identified in the fetal mice palate formation progression, including two reducing trends, two rising trends and five disordered trends. Next, the heatmap showed the miRNA expression from Clusters 4, 6, 9, 12 in the E13.5, E14.0, E14.5 and E15.0 groups. GO functional and KEGG pathway enrichment analysis found target genes of miRNAs in clusters involved in regulation of mesenchymal phenotype and the mitogen-activated protein kinase (MAPK) signaling pathway. Next, mesenchymal phenotype related miRNA-genes networks were constructed. The heatmap showing that the mesenchymal phenotype related miRNA expression of Clusters 4, 6, 9 and 12 at E13.5, E14.0, E14.5 and E15.0. Furthermore, the mesenchymal cell proliferation and apoptosis related miRNA-gene networks were identified in Clusters 6 and 12, including mmu-miR-504-3p-Hnf1b, etc. The expression level of mesenchymal cell proliferation and apoptosis related miRNAs at the E13.5, E14.0, E14.5, and E15.0 was verified by a RT-qPCR assay. CONCLUSIONS For the first time, we identified that clear dynamic miRNA expression during palate development. Furthermore, we demonstrated that mesenchymal cell proliferation and apoptosis related miRNAs, genes and the MAPK signaling pathway are important during fetal mice palate development.
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Affiliation(s)
- Meng Lu
- Department of Oral and Maxillofacial Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Laboratory of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian, China
| | - Feng Lu
- Department of Neurosurgery, Fujian Provincial Hospital, Fuzhou, Fujian, China
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Caiyu Liao
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Laboratory of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian, China
| | - Yan Guo
- Department of Oral and Maxillofacial Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Laboratory of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian, China
| | - Chuanqing Mao
- Department of Oral and Maxillofacial Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - Yongzhen Lai
- Department of Oral and Maxillofacial Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
- Fujian Key Laboratory of Oral Diseases & Fujian Provincial Engineering Research Center of Oral Biomaterial & Stomatological Key Laboratory of Fujian College and University, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, Fujian, China
| | - Xingyu Chen
- The First Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weihui Chen
- Department of Oral and Maxillofacial Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
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Nyirakanani C, Tamisier L, Bizimana JP, Rollin J, Nduwumuremyi A, Bigirimana VDP, Selmi I, Lasois L, Vanderschuren H, Massart S. Going beyond consensus genome sequences: An innovative SNP-based methodology reconstructs different Ugandan cassava brown streak virus haplotypes at a nationwide scale in Rwanda. Virus Evol 2023; 9:vead053. [PMID: 37692897 PMCID: PMC10491861 DOI: 10.1093/ve/vead053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023] Open
Abstract
Cassava Brown Streak Disease (CBSD), which is caused by cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), represents one of the most devastating threats to cassava production in Africa, including in Rwanda where a dramatic epidemic in 2014 dropped cassava yield from 3.3 million to 900,000 tonnes (1). Studying viral genetic diversity at the genome level is essential in disease management, as it can provide valuable information on the origin and dynamics of epidemic events. To fill the current lack of genome-based diversity studies of UCBSV, we performed a nationwide survey of cassava ipomovirus genomic sequences in Rwanda by high-throughput sequencing (HTS) of pools of plants sampled from 130 cassava fields in thirteen cassava-producing districts, spanning seven agro-ecological zones with contrasting climatic conditions and different cassava cultivars. HTS allowed the assembly of a nearly complete consensus genome of UCBSV in twelve districts. The phylogenetic analysis revealed high homology between UCBSV genome sequences, with a maximum of 0.8 per cent divergence between genomes at the nucleotide level. An in-depth investigation based on Single Nucleotide Polymorphisms (SNPs) was conducted to explore the genome diversity beyond the consensus sequences. First, to ensure the validity of the result, a panel of SNPs was confirmed by independent reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing. Furthermore, the combination of fixation index (FST) calculation and Principal Component Analysis (PCA) based on SNP patterns identified three different UCBSV haplotypes geographically clustered. The haplotype 2 (H2) was restricted to the central regions, where the NAROCAS 1 cultivar is predominantly farmed. RT-PCR and Sanger sequencing of individual NAROCAS1 plants confirmed their association with H2. Haplotype 1 was widely spread, with a 100 per cent occurrence in the Eastern region, while Haplotype 3 was only found in the Western region. These haplotypes' associations with specific cultivars or regions would need further confirmation. Our results prove that a much more complex picture of genetic diversity can be deciphered beyond the consensus sequences, with practical implications on virus epidemiology, evolution, and disease management. Our methodology proposes a high-resolution analysis of genome diversity beyond the consensus between and within samples. It can be used at various scales, from individual plants to pooled samples of virus-infected plants. Our findings also showed how subtle genetic differences could be informative on the potential impact of agricultural practices, as the presence and frequency of a virus haplotype could be correlated with the dissemination and adoption of improved cultivars.
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Affiliation(s)
- Chantal Nyirakanani
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Lucie Tamisier
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Jean Pierre Bizimana
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Johan Rollin
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Department of Research, DNAVision, Gosselies, Charleroi 6041, Belgium
| | - Athanase Nduwumuremyi
- Department of Research, Rwanda Agriculture and Animal Resources Development Board, Huye 5016, Rwanda
| | - Vincent de Paul Bigirimana
- Department of Crop Sciences, School of Agriculture and Food Sciences, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Musanze 210, Rwanda
| | - Ilhem Selmi
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Ludivine Lasois
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
| | - Hervé Vanderschuren
- Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
- Tropical Crop Improvement Laboratory, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven 3001, Belgium
| | - Sébastien Massart
- Integrated and Urban Plant Pathology Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux 5030, Belgium
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Lefebvre MN, Borcherding N, Reis RJ, Mou E, Liu V, Jabbari A. Molecular techniques drive cutting edge advancements in management of cutaneous T cell lymphoma. Front Immunol 2023; 14:1228563. [PMID: 37654486 PMCID: PMC10465366 DOI: 10.3389/fimmu.2023.1228563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Cutaneous 5T cell lymphoma (CTCL), characterized by malignant T cells infiltrating the skin with potential for dissemination, remains a challenging disease to diagnose and treat due to disease heterogeneity, treatment resistance, and lack of effective and standardized diagnostic and prognostic clinical tools. Currently, diagnosis of CTCL practically relies on clinical presentation, histopathology, and immunohistochemistry. These methods are collectively fraught with limitations in sensitivity and specificity. Fortunately, recent advances in flow cytometry, polymerase chain reaction, high throughput sequencing, and other molecular techniques have shown promise in improving diagnosis and treatment of CTCL. Examples of these advances include T cell receptor clonotyping via sequencing to detect CTCL earlier in the disease course and single-cell RNA sequencing to identify gene expression patterns that commonly drive CTCL pathogenesis. Experience with these techniques has afforded novel insights which may translate into enhanced diagnostic and therapeutic approaches for CTCL.
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Affiliation(s)
- Mitchell N. Lefebvre
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Dermatology, University of Iowa, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Ryan J. Reis
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Cancer Biology Graduate Program, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Eric Mou
- Department of Hematology and Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Vincent Liu
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, IA, United States
| | - Ali Jabbari
- University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Iowa City Veterans Affairs Medical Center, Iowa City, IA, United States
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Wang X, Huang M, Budowle B, Ge J. TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads. Front Genet 2023; 14:1227176. [PMID: 37533432 PMCID: PMC10390829 DOI: 10.3389/fgene.2023.1227176] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/13/2023] [Indexed: 08/04/2023] Open
Abstract
Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. Herein, a novel algorithm is described to retrieve TR regions from sequence alignment, and a software program TRcaller has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2 s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Availability: TRcaller is available at https://www.trcaller.com/SignIn.aspx.
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Affiliation(s)
- Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, United States
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
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20
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Froger-Lefebvre J, Lade Q, Vallier E, Bourgain C. E-prescription and invisible work in genomics in France. Front Sociol 2023; 8:1152364. [PMID: 37456272 PMCID: PMC10349168 DOI: 10.3389/fsoc.2023.1152364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
This article aims to analyze the transformations in medical prescription work and infrastructures brought by digitalization. Our fieldwork takes place in the context of precision medicine development based on genomics High Throughput Sequencing (HTS) in France, through the Plan France Médecine Génomique (PFMG 2025). The Plan aims at industrializing the production of genomic testing in clinical context at a national scale, particularly in oncology. To ensure the intensified flow of information between hospitals and HTS platforms required, a centralized process has been organized around two sequencing platforms and the introduction of a new e-prescription software (E-PRES). We start by analyzing how the e-prescription software changes the practices of health professionals by imposing new technological and professional standards. We show that, more than a mere prescription tool, this software is also a monitoring tool for the platforms and prescribers' work, and a support tool for the logistical and work organization. Secondly, we question the division of labor among the different professionals involved in the organizational or technical tasks required. We show that the feasibility of this new form of digitalized prescription relies on an important datawork performed by "small hands" to select, translate and process a vast amount of heterogeneous data.
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Affiliation(s)
- Juliette Froger-Lefebvre
- Groupe d'Etude des Méthodes de l'Analyse Sociologique de la Sorbonne, Centre National de la Recherche Scientifique, Paris, France
- Département SHS du Centre Léon Bérard, Lyon, France
| | - Quentin Lade
- Département SHS du Centre Léon Bérard, Lyon, France
- Centre de Recherche en Cancérologie de Lyon, Université Lyon 1, Lyon, France
| | - Estelle Vallier
- Département SHS du Centre Léon Bérard, Lyon, France
- Institut Gustave Roussy, Villejuif, France
| | - Catherine Bourgain
- Université Paris Cité, Centre National de la Recherche Scientifique, INSERM, Ecole des Hautes Etudes en Sciences Sociale, Centre de recherche médecine, sciences, santé, santé mentale, société, Villejuif, France
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21
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Liu Y, Chen P, Li W, Liu X, Yu G, Zhao H, Zeng S, Li M, Sun G, Feng Z. Conjunctive Analyses of BSA-Seq and BSR-Seq to Identify Candidate Genes Controlling the Black Lemma and Pericarp Trait in Barley. Int J Mol Sci 2023; 24:ijms24119473. [PMID: 37298424 DOI: 10.3390/ijms24119473] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
Black barley seeds are a health-beneficial diet resource because of their special chemical composition and antioxidant properties. The black lemma and pericarp (BLP) locus was mapped in a genetic interval of 0.807 Mb on chromosome 1H, but its genetic basis remains unknown. In this study, targeted metabolomics and conjunctive analyses of BSA-seq and BSR-seq were used to identify candidate genes of BLP and the precursors of black pigments. The results revealed that five candidate genes, purple acid phosphatase, 3-ketoacyl-CoA synthase 11, coiled-coil domain-containing protein 167, subtilisin-like protease, and caffeic acid-O-methyltransferase, of the BLP locus were identified in the 10.12 Mb location region on the 1H chromosome after differential expression analysis, and 17 differential metabolites, including the precursor and repeating unit of allomelanin, were accumulated in the late mike stage of black barley. Phenol nitrogen-free precursors such as catechol (protocatechuic aldehyde) or catecholic acids (caffeic, protocatechuic, and gallic acids) may promote black pigmentation. BLP can manipulate the accumulation of benzoic acid derivatives (salicylic acid, 2,4-dihydroxybenzoic acid, gallic acid, gentisic acid, protocatechuic acid, syringic acid, vanillic acid, protocatechuic aldehyde, and syringaldehyde) through the shikimate/chorismite pathway other than the phenylalanine pathway and alter the metabolism of the phenylpropanoid-monolignol branch. Collectively, it is reasonable to infer that black pigmentation in barley is due to allomelanin biosynthesis in the lemma and pericarp, and BLP regulates melanogenesis by manipulating the biosynthesis of its precursors.
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Affiliation(s)
- Yajie Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengzheng Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenshuo Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinchun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Guowu Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Hui Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuhua Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Mao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Zongyun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China/College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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22
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Chen P, Zhang G, Wang J. Editorial: Cancer diagnosis and novel drug discovery based on microbiome. Front Microbiol 2023; 14:1144986. [PMID: 37234541 PMCID: PMC10206304 DOI: 10.3389/fmicb.2023.1144986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/30/2023] [Indexed: 05/28/2023] Open
Affiliation(s)
- Peng Chen
- School of Pharmacy, Lanzhou University, Lanzhou, Gansu, China
| | - Ge Zhang
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhui Wang
- Department of Pathology, Yale University, New Haven, CT, United States
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23
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Amoia SS, Chiumenti M, Minafra A. First Identification of Fig Virus A and Fig Virus B in Ficus carica in Italy. Plants (Basel) 2023; 12:1503. [PMID: 37050129 PMCID: PMC10096765 DOI: 10.3390/plants12071503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/19/2023] [Accepted: 03/28/2023] [Indexed: 06/19/2023]
Abstract
Extracts of double-stranded RNA from three fig cultivars from an Apulian (Southern Italy) germplasm collection were used for high-throughput sequencing and revealed the presence of two distinct, recently described closteroviruses. Sequences obtained from these Apulian isolates belong to fig virus A and fig virus B and cover 38 and 25% of their RNA genome, respectively. Primer sets designed on selected contigs confirmed the presence of each virus in infected plants. A close phylogenetic relationship, investigated in a fragment of HSP70h protein, occurs among these isolates and the reference genomes. A nucleotide divergence (ranging from 10 to 30% along the different genes) was observed among our isolates and the reference genomes. This is the first finding of these virus species in autochthonous fig accessions in Europe.
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Affiliation(s)
- Serafina Serena Amoia
- Institute for Sustainable Plant Protection (IPSP)—National Research Council, 70126 Bari, Italy
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection (IPSP)—National Research Council, 70126 Bari, Italy
| | - Angelantonio Minafra
- Institute for Sustainable Plant Protection (IPSP)—National Research Council, 70126 Bari, Italy
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24
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Coelho MC, Malcata FX, Silva CCG. Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO). Foods 2023; 12:foods12050990. [PMID: 36900508 PMCID: PMC10000650 DOI: 10.3390/foods12050990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.
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Affiliation(s)
- Márcia C. Coelho
- School of Agrarian and Environmental Sciences, University of the Azores, 9700-042 Angra do Heroísmo, Portugal
| | - Francisco Xavier Malcata
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Oporto, Portugal
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Oporto, Portugal
| | - Célia C. G. Silva
- School of Agrarian and Environmental Sciences, University of the Azores, 9700-042 Angra do Heroísmo, Portugal
- Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, 9700-042 Angra do Heroísmo, Portugal
- Correspondence:
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25
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Mührer J, Lang-Muritano M, Lehmann R, Blouin JL, Schwitzgebel VM. Atypical familial diabetes associated with a novel NEUROD1 nonsense variant. J Pediatr Endocrinol Metab 2023; 36:101-104. [PMID: 36222545 DOI: 10.1515/jpem-2022-0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVES We aimed to identify the origin of atypical diabetes in a family with four generations of diabetes from South Asia. The family members showed different clinical phenotypes. Members of generation one to three were presumed to have type 2 diabetes and generation four to have type 1 diabetes. CASE PRESENTATION We performed a genetic analysis of the family using targeted high throughput sequencing. CONCLUSIONS We identified a novel nonsense variant in the neurogenic differentiation 1 (NEUROD1) gene, co-segregating with diabetes. The variant was located in the DNA-binding domain, altering a protein residue that was very well conserved among different species.
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Affiliation(s)
- Julia Mührer
- Division of Pediatric Endocrinology and Diabetology, University Children's Hospital, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Mariarosaria Lang-Muritano
- Division of Pediatric Endocrinology and Diabetology, University Children's Hospital, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Roger Lehmann
- Department of Endocrinology, Diabetes, and Clinical Nutrition and of Transplant Center, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Diagnostics, University Hospitals of Geneva, Geneva, Switzerland
| | - Valerie M Schwitzgebel
- Pediatric Endocrine and Diabetes Unit, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva Geneva, Switzerland.,Diabetes Center of the Faculty of Medicine, University of Geneva Geneva, Switzerland
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26
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Xu Z, Yu Z, Li S, Tian Z, Yuan J, You F. Exploration of the core gene signatures and mechanisms between NAFLD and sarcopenia through transcriptomic level. Front Endocrinol (Lausanne) 2023; 14:1140804. [PMID: 36967768 PMCID: PMC10033966 DOI: 10.3389/fendo.2023.1140804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
INTRODUCTION The increased prevalence of non-alcoholic fatty liver disease (NAFLD) and sarcopenia among the elderly are facing a significant challenge to the world's health systems. Our study aims to identify the coexpressed genes in NAFLD and sarcopenia patients. METHODS We downloaded the transcriptome data of NAFLD tissue from patients, as well as muscle tissues from sarcopenia patients, from the GEO database in order to investigate the shared transcriptional regulation mechanisms between these two diseases. Then, focusing on the genes that were frequently expressed in these diseases, together with GSVA and WGCNA, we utilized a range of analysis methods to identify the main co-expressed genes in both diseases by taking intersections. We investigated these changes after learning that they mostly affected lipid metabolism and oxidative stress injury pathways. RESULTS By analyzing these genes and their interactions with transcription factors and proteins, we were able to identify 8 genes that share common patterns. From these 8 genes, we were possible to forecast potential future medicines. Our research raises the possibility of NAFLD and sarcopenia transcriptome regulatory pathways in aging populations. DISCUSSION In conclusion, a complete transcription pattern mapping was carried out in order to identify the core genes, underlying biological mechanisms, and possible therapeutic targets that regulate aging in NAFLD and sarcopenia patients. It provides novel insights and proof in favor of decreasing the increased prevalence of sarcopenia in the elderly caused by NAFLD.
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Affiliation(s)
- Ziying Xu
- School of Basic Medical Sciences, Peking University, Beijing, China
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shang Li
- Department of Orthopedics, General Hospital of Chinese People's Liberation Army of China (PLA), Beijing, China
- National Clinical Research Center for Orthopedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Jing Yuan, ; Fuping You,
| | - Fuping You
- School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Jing Yuan, ; Fuping You,
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27
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Koizumi Y, Ichijo T, Uchii K, Nasu M. Changes in bacterial diversity and community structure in drinking water distribution system revealed by high throughput sequencing. J Microorg Control 2023; 28:27-34. [PMID: 37277955 DOI: 10.4265/jmc.28.1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
For microbiological management of water quality, it is important to identify bacteria and to understand the community structure. To analyze the community structure during water purification and distribution, we selected a distribution system in which water from other water treatment facilities was not mixed with the target water. Changes in the bacterial community structure during treatment and distribution processes in a slow filtration water treatment facility were analyzed using 16S rRNA gene amplicon sequencing with a portable sequencer MinION. The microbial diversity was reduced by chlorination. The genus level diversity increased during distribution and this diversity was maintained through to the terminal tap water. Yersinia and Aeromonas were dominant in the intake water, and Legionella was dominant in the slow sand filtered water. Chlorination greatly reduced the relative abundance of Yersinia, Aeromonas, and Legionella, and these bacteria were not detected in the terminal tap water. Sphingomonas, Starkeya and Methylobacterium became dominant in the water after chlorination. These bacteria could be used as important indicator bacteria to provide useful information for microbiological control in drinking water distribution systems.
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Affiliation(s)
- Yoshihiko Koizumi
- Environmental Health Section, Osaka Institute of Public Health
- Graduate School of Pharmaceutical Sciences, Osaka Ohtani University
| | - Tomoaki Ichijo
- Faculty of Health and Nutrition, Osaka Shoin Women's University
- Graduate School of Human Sciences, Osaka Shoin Women's University
| | | | - Masao Nasu
- Graduate School of Pharmaceutical Sciences, Osaka Ohtani University
- Osaka University
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28
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Han J, Zhang Z, Zhang Z, Yang S. Corrigendum: Artemisinin relieves myocardial ischemia-reperfusion injury via modulating miR-29b-3p and hemicentin 1. Front Pharmacol 2023; 14:1169734. [PMID: 36937868 PMCID: PMC10015591 DOI: 10.3389/fphar.2023.1169734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fphar.2022.918966.].
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Affiliation(s)
- Junyu Han
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ziguan Zhang
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhonghe Zhang
- Department of Cardiology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shuyu Yang
- Xiamen Diabetes Institute, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
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29
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Abrahamian P, Cai W, Nunziata SO, Ling KS, Jaiswal N, Mavrodieva VA, Rivera Y, Nakhla MK. Comparative Analysis of Tomato Brown Rugose Fruit Virus Isolates Shows Limited Genetic Diversity. Viruses 2022; 14. [PMID: 36560820 DOI: 10.3390/v14122816] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Tomato is an important vegetable in the United States and around the world. Recently, tomato brown rugose fruit virus (ToBRFV), an emerging tobamovirus, has impacted tomato crops worldwide and can result in fruit loss. ToBRFV causes severe symptoms, such as mosaic, puckering, and necrotic lesions on leaves; other symptoms include brown rugose and marbling on fruits. More importantly, ToBRFV can overcome resistance in tomato cultivars carrying the Tm-22 locus. In this study, we recovered ToBRFV sequences from tomato seeds, leaves, and fruits from the U.S., Mexico, and Peru. Samples were pre-screened using a real-time RT-PCR assay prior to high-throughput sequencing. Virus draft genomes from 22 samples were assembled and analyzed against more than 120 publicly available genomes. Overall, most sequenced isolates were similar to each other and did not form a distinct population. Phylogenetic analysis revealed three clades within the ToBRFV population. Most of the isolates (95%) clustered in clade 3. Genetic analysis revealed differentiation between the three clades indicating minor divergence occurring. Overall, pairwise identity showed limited genetic diversity among the isolates in this study with worldwide isolates, with a pairwise identity ranging from 99.36% and 99.97%. The overall population is undergoing high gene flow and population expansion with strong negative selection pressure at all ToBRFV genes. Based on the results of this study, it is likely that the limited ToBRFV diversity is associated with the rapid movement and eradication of ToBRFV-infected material between countries.
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30
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Qin M, Fu Y, Li N, Zhao Y, Yang B, Wang L, Ouyang S. Effects of Wheat Tempering with Slightly Acidic Electrolyzed Water on the Microbiota and Flour Characteristics. Foods 2022; 11:foods11243990. [PMID: 36553732 PMCID: PMC9777789 DOI: 10.3390/foods11243990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Slightly acidic electrolyzed water (SAEW) was prepared and used as wheat tempering water. This study explored the impacts of tempering with SAEW on microbial load and diversity and quality properties of wheat flour. As SAEW volume ratio increased, the residual level of total plate counts (TPC) and mould/yeast counts (MYC) decreased dramatically (p < 0.05). Based on genomics analysis, bacterial 16S rRNA gene and fungal ITS1 gene region were performed to characterize the changes in microbial communities’ composition and diversity in response to SAEW treatment. SAEW optimal volume ratio (6.5:10, v/v) of SAEW with distilled water influenced wheat microbiome composition, with a higher microbial diversity and abundance discovered on the control grains. Bacteroidetes of predominant bacterial phylum and Ascomycota of the most abundant fungal phylum were reduced after SAEW optimal volume ratio tempering. The flour yield is higher and ash content is lower than the control samples. Falling number and “b*” in terms of colour markedly increased. DSC (Differential Scanning Calorimetry) test showed that To (onset temperature), Tp (peak temperature), and Tc (conclusion temperature) were significantly decreased in thermal characteristics of flour. Gluten content, protein content, ΔH and pasting properties tests showed no significant change. It can be concluded that SAEW should be applied on wheat tempering for producing clean wheat flour. ANOVA and Tukey’s honestly significant difference (HSD) test were used for the analysis of variance and differences between the experimental and control groups, with p < 0.05.
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Affiliation(s)
- Mingqian Qin
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yingwu Fu
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Ning Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yinyin Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Li Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, China
| | - Shaohui Ouyang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
- Engineering Research Center of Grain and Oil Functionalized Processing in Universities of Shaanxi Province, Yangling, Xianyang 712100, China
- Correspondence:
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31
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Wu C, Narale DD, Cui Z, Wang X, Liu H, Xu W, Zhang G, Sun J. Diversity, structure, and distribution of bacterioplankton and diazotroph communities in the Bay of Bengal during the winter monsoon. Front Microbiol 2022; 13:987462. [PMID: 36532434 PMCID: PMC9748438 DOI: 10.3389/fmicb.2022.987462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/03/2022] [Indexed: 10/31/2023] Open
Abstract
The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding "new" nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.
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Affiliation(s)
- Chao Wu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dhiraj Dhondiram Narale
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Zhengguo Cui
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xingzhou Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Haijiao Liu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
| | - Wenzhe Xu
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
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Zhi W, Tang K, Yang J, Yang T, Chen R, Huang J, Tan H, Zhao J, Sheng Z. Research on the Gut Microbiota of Hainan Black Goat. Animals (Basel) 2022; 12:ani12223129. [PMID: 36428357 PMCID: PMC9686789 DOI: 10.3390/ani12223129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The intestine of animals is a complex micro-ecosystem containing a large number of microbiomes, which is essential for the host's health development. The Hainan black goat with good resistance and adaptability is a unique species in Hainan, China. These unique physiological characteristics are inseparable from their intestinal microbiota. In this study, high-throughput sequencing was used to investigate bacterial communities in different segments of the intestinal tract of Hainan black goat. The results showed that the indices of Chao1 and ACE in the cecum and colon were significantly greater than those in the ileum (p = 0.007, 0.018). According to PCoA, the intestinal flora composition of the cecum and colon is almost equivalent. In contexts of the phylum, Firmicutes, Bacteroidota, and Pseudomonadota were the dominant phyla in the gut of the Hainan black goat. While in context of the genus, the dominant groups in the gut of black goats mainly include Ruminococcaceae_UCG-005, Bacteroides, Paeniclostridium, Christensenellaceae_R-7_group, Rikenellaceae_RC9_gut_group, and Eubacterium coprostanoligenes _group, Prevotella_1, they have different proportions in different intestinal segments. The gut microbiota of Hainan black goat is mainly Firmicutes, Bacteroidota, and Pseudomonadota. Influenced by the intestinal location where they colonize, the large intestine has a more complex intestinal flora than the small intestine. In contrast, there are only minor differences between the caecum and the colon in the large intestine.
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Affiliation(s)
- Wenbo Zhi
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Kai Tang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Jinsong Yang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
- Correspondence: (J.Y.); (Z.S.)
| | - Tianshu Yang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Rong Chen
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Jiaming Huang
- College of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Haisheng Tan
- College of Materials Science and Engineering, Hainan University, Haikou 570228, China
| | - Jianguo Zhao
- Laboratory of Tropical Veterinary Medicine and Vector Biology, School of Life Sciences, Hainan University, Haikou 570228, China
| | - Zhanwu Sheng
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (J.Y.); (Z.S.)
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Liu T, Guo S, Wu C, Zhang R, Zhong Q, Shi H, Zhou R, Qin Y, Jin Y. Phyllosphere microbial community of cigar tobacco and its corresponding metabolites. Front Microbiol 2022; 13:1025881. [PMID: 36439836 PMCID: PMC9691965 DOI: 10.3389/fmicb.2022.1025881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 08/29/2023] Open
Abstract
Cigar is made of a typical fermented tobacco where the microbiota inhabits within an alkaline environment. Our current understanding on cigar fermentation is far from thorough. This work employed both high-throughput sequencing and chromatography-mass spectrometric technologies to provide new scientific reference for this specific fermented system. Typical cigar samples from different regions (the Caribbeans, South America, East Asia, and Southeast Asia) were investigated. The results show that Firmicutes, Actinobacteria, Proteobacteria, Ascomycota, and Basidiomycota were the predominant phyla in the cigar samples. Rather than the fungal community, it was the bacterial community structures that played vital roles to differentiate the cigar from different regions: Staphylococcus was the dominant genus in the Americas; Bacillus was the dominant genus in Southeast Asia; while in East Asia, there was no dominant genus. Such differences in community structure then affected the microflora metabolism. The correlation between microbiota and metabolites revealed that Aspergillaceae, Cercospora, and Staphylococcus were significantly correlated with sclareolide; Bacillus were positively associated with isophorone. Alcaligenaceae was significantly and positively correlated with L-nicotine and hexadecanoic acid, methyl ester. GRAPHICAL ABSTRACT.
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Affiliation(s)
- Tiantian Liu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Shiping Guo
- R&D Department, Sichuan Provincial Branch of China National Tobacco Crop Tobacco Science Institute, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Ruina Zhang
- R&D Department, Deyang Tobacco Company of Sichuan Province, Sichuan, Deyang, China
| | - Qiu Zhong
- R&D Department, Deyang Tobacco Company of Sichuan Province, Sichuan, Deyang, China
| | - Hongzhi Shi
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Yanqing Qin
- R&D Department, Sichuan Provincial Branch of China National Tobacco Crop Tobacco Science Institute, Chengdu, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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Lorenzo-Rebenaque L, Casto-Rebollo C, Diretto G, Frusciante S, Rodríguez JC, Ventero MP, Molina-Pardines C, Vega S, Marin C, Marco-Jiménez F. Examining the effects of Salmonella phage on the caecal microbiota and metabolome features in Salmonella-free broilers. Front Genet 2022; 13:1060713. [PMID: 36437955 PMCID: PMC9691336 DOI: 10.3389/fgene.2022.1060713] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 10/29/2023] Open
Abstract
Bacteriophages selectively infect and kill their target bacterial host, being a promising approach to controlling zoonotic bacteria in poultry production. To ensure confidence in its use, fundamental questions of safety and toxicity monitoring of phage therapy should be raised. Due to its high specificity, a minimal impact on the gut ecology is expected; however, more in-depth research into key parameters that influence the success of phage interventions has been needed to reach a consensus on the impact of bacteriophage therapy in the gut. In this context, this study aimed to investigate the interaction of phages with animals; more specifically, we compared the caecum microbiome and metabolome after a Salmonella phage challenge in Salmonella-free broilers, evaluating the role of the phage administration route. To this end, we employed 45 caecum content samples from a previous study where Salmonella phages were administered via drinking water or feed for 24 h from 4, 5 to 6-weeks-old broilers. High-throughput 16S rRNA gene sequencing showed a high level of similarity (beta diversity) but revealed a significant change in alpha diversity between broilers with Salmonella-phage administered in the drinking water and control. Our results showed that the phages affected only a few genera of the microbiota's structure, regardless of the administration route. Among these, we found a significant increase in Streptococcus and Sellimonas in the drinking water and Lactobacillus, Anaeroplasma and Clostridia_vadinBB60_group in the feed. Nevertheless, the LC-HRMS-based metabolomics analyses revealed that despite few genera were significantly affected, a substantial number of metabolites, especially in the phage administered in the drinking water were significantly altered (64 and 14 in the drinking water and feed groups, respectively). Overall, our study shows that preventive therapy with bacteriophages minimally alters the caecal microbiota but significantly impacts their metabolites, regardless of the route of administration.
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Affiliation(s)
- Laura Lorenzo-Rebenaque
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Cristina Casto-Rebollo
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
| | - Gianfranco Diretto
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Sarah Frusciante
- Italian Agency for New Technologies, Energy and Sustainable Development (ENEA), Biotechnology Laboratory, Centro Ricerche Casaccia, Santa Maria di Galeria, Rome, Italy
| | - Juan Carlos Rodríguez
- Microbiology Department, Balmis General University Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, Alicante, Spain
| | - María-Paz Ventero
- Microbiology Department, Balmis General University Hospital, ISABIAL, Alicante, Spain
| | | | - Santiago Vega
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Clara Marin
- Department of Animal Production and Health, Veterinary Public Health and Food Science and Technology, Biomedical Research Institute, Faculty of Veterinary Medicine, Cardenal Herrera-CEU University, CEU Universities, Valencia, Spain
| | - Francisco Marco-Jiménez
- Institute of Science and Animal Technology, Universitat Politècnica de València, Valencia, Spain
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Petrzik K, Přibylová J, Špak J, Sarkisova T, Fránová J, Holub J, Skalík J, Koloniuk I. Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus. Viruses 2022; 14:v14112456. [PMID: 36366554 PMCID: PMC9697673 DOI: 10.3390/v14112456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3 ́- N-P´-P-P3-M-G-L -5 ́. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75 %) with strawberry virus 2. BCRV2 was detected in Cryptomyzusgaleopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host.
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Affiliation(s)
- Karel Petrzik
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
- Correspondence:
| | - Jaroslava Přibylová
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | - Josef Špak
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | - Tatiana Sarkisova
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | - Jana Fránová
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | - Jan Holub
- Jan Holub Ltd., Hvozdečko 7, 783 25 Bouzov, Czech Republic
| | - Jan Skalík
- Jan Holub Ltd., Hvozdečko 7, 783 25 Bouzov, Czech Republic
| | - Igor Koloniuk
- Biology Centre Academy of Sciences of the Czech Republic, Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
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Temple C, Blouin AG, De Jonghe K, Foucart Y, Botermans M, Westenberg M, Schoen R, Gentit P, Visage M, Verdin E, Wipf-Scheibel C, Ziebell H, Gaafar YZA, Zia A, Yan XH, Richert-Pöggeler KR, Ulrich R, Rivarez MPS, Kutnjak D, Vučurović A, Massart S. Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time. Plant Dis 2022; 106:2797-2807. [PMID: 35394335 DOI: 10.1094/pdis-12-21-2800-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Coline Temple
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
- Plant Protection Department, Agroscope, 1260 Nyon, Switzerland
| | - Kris De Jonghe
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Marleen Botermans
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Marcel Westenberg
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Ruben Schoen
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Pascal Gentit
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Michèle Visage
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Catherine Wipf-Scheibel
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Xiao-Hua Yan
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | | | - Mark Paul S Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
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Abstract
In 2020, a novel agent was discovered in strawberry, a rhabdovirus closely related to lettuce necrotic yellows virus. The new virus, named strawberry virus 2 (StrV-2), was discovered in an accession of the Fragaria virus collection of the National Clonal Germplasm Repository (NCGR), and for this reason, it was studied in-depth. The complete StrV-2 genome was obtained and investigated in silico. Transmission was assessed using two aphid species whereas a multiplex RT-PCR test targeting plant and virus genes was developed and used to screen the NCGR Fragaria virus collection.
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Affiliation(s)
- Ava Medberry
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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Abstract
BACKGROUND Robust analysis of DNA sequencing data needs to include a set of quality control steps to ensure that technical bias is kept to a minimum. A metric easily obtained is the frequency of each of the nucleobases for each position across all sequencing reads. Here, we explore the differences in nucleobase compositions of various library types produced by standard experimental methodologies. Methods: We obtained the compositions of nearly 3000 publicly available datasets and subjected them to Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction for a two-dimensional representation of their composition characteristics. Results: We find that most library types result in a specific composition profile. We use this to give an estimate of how strongly the composition of a test library resembles the profiles of previously published libraries, and how likely the test sample is to be of a particular type. We introduce Librarian, a user-friendly web application and command line tool which enables checking base compositions of test libraries against known library types. Conclusions: Library preparation methods strongly influence the per position nucleobase content. By comparing test libraries to a database of previously published library types we can make predictions regarding the library preparation method. Librarian is a user-friendly tool to access this information for quality assurance purposes as discrepancies can flag potential irregularities very early on.
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Affiliation(s)
| | - Caroline Gaud
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Christel Krueger
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
- Bioinformatics, Altos Labs Cambridge Institute of Science, Cambridge, CB21 6GP, UK
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Vashishtha K, Gaud C, Andrews S, Krueger C. Librarian: A quality control tool to analyse sequencing library compositions. F1000Res 2022; 11:1122. [PMID: 36300036 PMCID: PMC9579741 DOI: 10.12688/f1000research.125325.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 01/27/2024] Open
Abstract
Background Robust analysis of DNA sequencing data needs to include a set of quality control steps to ensure that technical bias is kept to a minimum. A metric easily obtained is the frequency of each of the nucleobases for each position across all sequencing reads. Here, we explore the differences in nucleobase compositions of various library types produced by standard experimental methodologies. Methods We obtained the compositions of nearly 3000 publicly available datasets and subjected them to Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction for a two-dimensional representation of their composition characteristics. Results We find that most library types result in a specific composition profile. We use this to give an estimate of how strongly the composition of a test library resembles the profiles of previously published libraries, and how likely the test sample is to be of a particular type. We introduce Librarian, a user-friendly web application and command line tool which enables checking base compositions of test libraries against known library types. Conclusions Library preparation methods strongly influence the per position nucleobase content. By comparing test libraries to a database of previously published library types we can make predictions regarding the library preparation method. Librarian is a user-friendly tool to access this information for quality assurance purposes as discrepancies can flag potential irregularities very early on.
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Affiliation(s)
| | - Caroline Gaud
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Christel Krueger
- Bioinformatics, Babraham Institute, Cambridge, CB22 3AT, UK
- Bioinformatics, Altos Labs Cambridge Institute of Science, Cambridge, CB21 6GP, UK
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40
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Wang S, Tan Y, Li S, Zhu T. Structural and Dynamic Analysis of Leaf-Associated Fungal Community of Walnut Leaves Infected by Leaf Spot Disease Based Illumina High-Throughput Sequencing Technology. Pol J Microbiol 2022; 71:429-441. [PMID: 36185023 PMCID: PMC9608163 DOI: 10.33073/pjm-2022-038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Leaf-associated microbiota is vital in plant-environment interactions and is the basis for micro-ecological regulation. However, there are no studies on the direct differences in microbial community composition between disease-susceptible and healthy walnut leaves. This study collected five samples of healthy and infected leaves (all leaves with abnormal spots were considered diseased leaves) from May to October 2018. Differences in fungal diversity (Chao1 index, Shannon index, and Simpson index) and community structure were observed by sequencing and analyzing diseased and healthy leaf microbial communities by Illumina HiSeq sequencing technology. The main fungal phyla of walnut leaf-associated were Ascomycota, Basidiomycota, and Glomeromycota. Diversity indices (Shannon and Chao1 index values) of healthy leaves differed significantly in the late stages of disease onset. The results showed that the fungal species that differed considerably between the healthy and infected groups differed, and the fungal species that differed significantly between the healthy and infected groups changed with the development of the leaf disease. Critical control time points were determined by analyzing the population dynamics of pathogenic fungi. Leaf-associated microorganisms are abundant and diverse, and fungal identification and diversity studies are helpful for developing more appropriate walnut management strategies.
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Affiliation(s)
- Shiwei Wang
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Yu Tan
- College of Forestry, Sichuan Agricultural University, Chengdu, China,Chengdu Botanical Garden, Chengdu, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu, China,National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Chengdu, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu, China, T. Zhu, College of Forestry, Sichuan Agricultural University , Chengdu, China # Shiwei Wang and Yu Tan contribute equally to this work and are co-first authors.
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41
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Williamson BD, Hughes JP, Willis AD. A multiview model for relative and absolute microbial abundances. Biometrics 2022; 78:1181-1194. [PMID: 34048057 PMCID: PMC8982138 DOI: 10.1111/biom.13503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 12/30/2022]
Abstract
The absolute abundance of bacterial taxa in human host-associated environments plays a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species are comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a study of the effect of HIV acquisition on microbial abundances, and a sensitivity study where we jackknife the taxa with observed absolute abundances.
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Affiliation(s)
| | - James P. Hughes
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Amy D. Willis
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
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Mulenga RM, Miano DW, Al Rwahnih M, Kaimoyo E, Akello J, Nzuve FM, Simulundu E, Alabi T, Chikoti PC, Alabi OJ. Survey for Virus Diversity in Common Bean ( Phaseolus vulgaris) Fields and the Detection of a Novel Strain of Cowpea polerovirus 1 in Zambia. Plant Dis 2022; 106:2380-2391. [PMID: 35188414 DOI: 10.1094/pdis-11-21-2533-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The production of common bean (Phaseolus vulgaris L.) is adversely affected by virus-like diseases globally, but little is known about the occurrence, distribution, and diversity of common bean-infecting viruses in Zambia. Consequently, field surveys were conducted during the 2018 season in 128 fields across six provinces of Zambia and 640 common bean leaf tissue samples were collected with (n = 585) or without (n = 55) symptoms. The prevalence of symptomatic fields was 100%, but incidence of symptomatic plants ranged from 32 to 67.5%. Metagenomic analyses of nine composite samples and a single plant sample of interest revealed the occurrence of isolates of Bean common mosaic necrosis virus, Bean common mosaic virus, Cowpea aphid-borne mosaic virus, Peanut mottle virus, Southern bean mosaic virus (SBMV), Cucumber mosaic virus, Phaseolus vulgaris alphaendornavirus 1 (PvEV-1), PvEV-2, Ethiopian tobacco bushy top virus (ETBTV), and a novel strain of Cowpea polerovirus 1 (CPPV1-Pv) of 5,902 nt in length. While CPPV1-Pv was consistently detected in mixed infection with ETBTV and its satellite RNA molecule, based on results of mechanical transmission assays it does not appear to be involved in disease etiology, suggesting that its role may be limited to being a helper virus for the umbravirus. Screening of the survey samples by real-time PCR for the viruses detected by high-throughput sequencing revealed the prevalence of single (65.2% or 417/640) over mixed (1.9% or 12/640) infections in the samples. SBMV was the most frequently detected virus, occurring in ∼29.4% (188/640) of the samples and at a prevalence rate of 58.6% (75/128) across fields. The results showed that diverse virus species are present in Zambian common bean fields and the information will be useful for the management of common bean viral diseases.
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Affiliation(s)
- Rabson M Mulenga
- Zambia Agriculture Research Institute, Chilanga, 10101 Lusaka, Zambia
- Department of Plant Sciences and Crop Protection, University of Nairobi, Nairobi 00625, Kenya
| | - Douglas W Miano
- Department of Plant Sciences and Crop Protection, University of Nairobi, Nairobi 00625, Kenya
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Evans Kaimoyo
- School of Biological Sciences, Great East Road Campus, University of Zambia, 10101 Lusaka, Zambia
| | - Juliet Akello
- School of Veterinary Medicine, Great East Road Campus, University of Zambia, 10101 Lusaka, Zambia
| | - Felister M Nzuve
- Department of Plant Sciences and Crop Protection, University of Nairobi, Nairobi 00625, Kenya
| | - Edgar Simulundu
- International Institute of Tropical Agriculture, Southern African Research Hub, Chongwe District 10100, Lusaka Province, Zambia
| | - Tunrayo Alabi
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Chilanga, 10101 Lusaka, Zambia
| | - Olufemi J Alabi
- Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596, U.S.A
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Zhu L, Li L, Yang Q, Chen L, Zhang L, Zhang G, Lin B, Tang J, Zhang Z, Chen S. Study on microbial community of "green-covering" Tuqu and the effect of fortified autochthonous Monascus purpureus on the flavor components of light-aroma-type Baijiu. Front Microbiol 2022; 13:973616. [PMID: 36060768 PMCID: PMC9434108 DOI: 10.3389/fmicb.2022.973616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
"Green-covering" Tuqu (TQ), as one of Xiaoqu, is a special fermentative starter (also known as Jiuqu in Chinese) that originated in southern China and is characterized by a layer of green mold covering (Aspergillus clavatus) the surface and (sometimes) with a red heart. It plays a vital role in producing light-aroma-type Baijiu (LATB). However, to date, the microbiota that causes red heart of TQ remain largely unexplored, and it is still unclear how these microbiota influence on the quality of LATB. In this study, two types of TQ, one with a red heart (RH) and another with a non-red heart (NRH), were investigated by high throughput sequencing (HTS) and directional screening of culture-dependent methods. The obtained results revealed the differences in the microbial communities of different TQ and led to the isolation of two species of Monascus. Interestingly, the results of high performance liquid chromatography (HPLC) detection showed that citrinin was not detected, indicating that Monascus isolated from TQ was no safety risk, and the contents of gamma-aminobutyric acid in the fermented grains of RH were higher than that of NRH during the fermentation. Selecting the superior autochthonous Monascus (M1) isolated from the TQ to reinoculate into the TQ-making process, established a stable method for producing the experimental "red heart" Tuqu (ERH), which confirmed that the cause of "red heart" was the growth of Monascus strains. After the lab-scale production test, ERH increased ethyl ester production and reduced higher alcohols production. In addition, Monascus had an inhibitory effect on the growth of Saccharomyces and Aspergillus. This study provides the safe, health-beneficial, and superior fermentation strains and strategies for improving the quality of TQ and LATB.
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Affiliation(s)
- Liping Zhu
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Lanqi Li
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Qiang Yang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Liang Chen
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Lei Zhang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Gang Zhang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Bin Lin
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Jie Tang
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
| | - Zongjie Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, Huangshi, China
| | - Shenxi Chen
- Hubei Key Laboratory of Quality and Safety of Traditional Chinese Medicine and Health Food, Jing Brand Co. Ltd, Daye, China
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Kamilari E, Tsaltas D, Stanton C, Ross RP. Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses. Foods 2022; 11:2483. [PMID: 36010485 PMCID: PMC9407514 DOI: 10.3390/foods11162483] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses-namely Greek and Cypriot-using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.
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Affiliation(s)
- Eleni Kamilari
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
| | - Dimitrios Tsaltas
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
- Department of Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Co., P61 C996 Cork, Ireland
| | - R. Paul Ross
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland or
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland
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45
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Xu M, Risse J, Kormelink R. Cap-snatching as a possible contributor to photosynthesis shut-off. J Gen Virol 2022; 103. [PMID: 35947091 DOI: 10.1099/jgv.0.001763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cap-snatching is a mechanism applied by segmented, negative strand (-) RNA viruses (NSVs) to initiate genome transcription. So far, the cap donor source of cytoplasmic-replicating NSVs has remained elusive. Recently, studies pointed to processing body (P body, PB) as the potential source for providing capped RNAs but conclusive evidence is still lacking. To attempt identifying these sources, here the 5' non-viral leader sequences of Tomato spotted wilt virus (TSWV) N mRNAs were analysed by high-throughput sequencing (HTS) from plants subjected to normal and heat-stress conditions, and subsequently mapped on host donor transcripts. The majority of non-viral heterogenous, host-derived leader sequences ranged in size between ~10-20 nt and contained A or AG residues at the cleavage site and the presence of certain sequence motifs. Mapping the capped-leader sequences to the 5' UTR region of genes encoded by the Nicotiana tabacum genome, identified 348 donor genes and which were specifically enriched in cellular photosynthesis pathway. Nineteen of those were clearly expressed differentially at normal condition versus heat-stress conditions. Although the results did not point towards snatching of capped-RNA leader sequences from certain cytoplasmic RNA granules in particular, they indicated photosynthesis downregulation (and development of disease symptoms) partially result from cap-snatching.
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Affiliation(s)
- Min Xu
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Judith Risse
- Laboratory of Bioinformatics, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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Çelik I, Keskin E. Revealing the Microbiome of Four Different Thermal Springs in Turkey with Environmental DNA Metabarcoding. Biology (Basel) 2022; 11:biology11070998. [PMID: 36101376 PMCID: PMC9311576 DOI: 10.3390/biology11070998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The physicochemical conditions of thermal springs are one of the most significant barriers for detecting microbial life. According to the findings of various studies, high-throughput DNA sequencing technology can be utilized to perform more precise and detailed microbiome assessments. The main goal of this paper was to determine the microbiome in a thermal spring by metabarcoding environmental DNA obtained from four different sources and revealing how temperature and chemical composition affect the microbiome. This research also aimed to gather information that will aid in determining the best gene region and bioinformatic pipeline. The findings revealed a link between four different thermal springs’ physicochemical parameters and microbial composition and we found various manipulable steps in this study. This research is also first comprehensive thermal spring metabarcoding study conducted in Turkey. Abstract One of the most significant challenges for detecting microbial life in thermal springs by conventional techniques such as culturing is these places’ physicochemical (temperature, heavy metal content, pH, etc.) conditions. Data from several studies suggest that high-throughput DNA sequencing technologies can be used to perform more accurate and detailed microbiome analyses. The primary aim of this paper was to determine the microbiome in the thermal source by metabarcoding environmental DNA isolated from four different sources and reveal the reflection of differences caused by temperature and chemical content on the microbiome. DNA was extracted from water filtered with enclosed filters and using the Illumina high-throughput sequencing platform, V3 and V4 regions of the 16S rRNA gene were sequenced. The results showed a correlation between physicochemical conditions and microorganism composition of four different thermal springs. Springs with extremely high temperature (89–90 °C) were dominated by hyperthermophiles such as Hydrogenobacter and Thermus, while a spring with a high temperature (52 °C) was dominated by thermophiles such as Thermoanaerobaculum and Desulfurispora, and a spring with a low temperature (26 °C) and high salinity was dominated by halophiles and sulfur-oxidizers such as Hydrogenovibrio and Sulfirimonas. With this research, we observed many manipulable steps according to the work of interest. This study sought to obtain data that will help decide the right gene region and choose the optimal bioinformatic pipeline.
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Affiliation(s)
- Işılay Çelik
- Biotechnology Institute, Ankara University, Ankara 06135, Turkey;
- Evolutionary Genetics Laboratory (eGL), Department of Fisheries and Aquaculture, Agricultural Faculty, Ankara University, Ankara 06135, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Department of Fisheries and Aquaculture, Agricultural Faculty, Ankara University, Ankara 06135, Turkey
- Correspondence:
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Li J, Yao X, Yao Y, An L, Feng Z, Wu K. Genome-Wide Association Mapping of Hulless Barely Phenotypes in Drought Environment. Front Plant Sci 2022; 13:924892. [PMID: 35812943 PMCID: PMC9260272 DOI: 10.3389/fpls.2022.924892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Drought stress is one of the main factors restricting hulless barley (Hordeum vulgare L. var. nudum Hook. f.) yield. Genome-wide association study was performed using 269 lines of hulless barley to identify single-nucleotide polymorphism (SNP) markers associated with drought-resistance traits. The plants were cultured under either normal or drought conditions, and various quantitative traits including shoot fresh weight, shoot dry weight, root fresh weight, root dry weight, leaf fresh weight, leaf saturated fresh weight, leaf dry weight, ratio of root and shoot fresh weight, ratio of root and shoot dry weight, shoot water loss rate, root water loss rate, leaf water content and leaf relative water content, and field phenotypes including main spike length, grain number per plant, grain weight per plant, thousand grain weight (TGW), main spike number, plant height, and effective spike number of plants were collected. After genotyping the plants, a total of 8,936,130 highly consistent population SNP markers were obtained with integrity > 0.5 and minor allele frequency > 0.05. Eight candidate genes potentially contributed to the hulless barley drought resistance were obtained at loci near significant SNPs. For example, EMB506, DCR, and APD2 genes for effective spike number of plants, ABCG11 gene for main spike number (MEN), CLPR2 gene for main spike length, YIP4B gene for root and shoot dry weight (RSWD), and GLYK and BTS genes for TGW. The SNPs and candidate genes identified in this study will be useful in hulless barley breeding under drought resistance.
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Affiliation(s)
- Jie Li
- College of Agronomy Sichuan Agricultural University, Chengdu, China
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Xiaohua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Youhua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Likun An
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Zongyun Feng
- College of Agronomy Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| | - Kunlun Wu
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
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Pan Y, Li G, Su L, Zheng P, Wang Y, Shen Z, Chen Z, Han Q, Gong J. Seagrass Colonization Alters Diversity, Abundance, Taxonomic, and Functional Community Structure of Benthic Microbial Eukaryotes. Front Microbiol 2022; 13:901741. [PMID: 35770161 PMCID: PMC9234489 DOI: 10.3389/fmicb.2022.901741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Seagrass form high productive ecosystems in coastal environments. However, the effects of these coastal plants on the structure and function of the belowground eukaryotic microbiome remain elusive. In this study, we characterized the community of microbial eukaryotes (microeukaryotes) in both vegetated and unvegetated sediments using 18S rRNA gene amplicon sequencing and quantitative PCR. Analysis of sequencing data showed that the eelgrass (Zostera marina) colonization decreased the alpha diversity indices of benthic microeukaryotes. Apicomplexa represented an average of 83% of reads across all samples, with a higher proportion at the vegetated sites. The taxonomic community structure was significantly different between these two types of sediments, for which the concentration ofNH 4 + in sediment porewater and salinity could account. Phylogenetic analyses of long 18S rRNA genes (around 1,030 bp) indicated these apicomplexan parasites are closely related to gregarine Lecudina polymorpha. Determination of 18S rRNA gene abundances provided evidence that the eelgrass markedly promoted the biomass of the gregarine and all microeukaryotes in the seagrass-colonized sediments and confirmed that the gregarine was hosted by a polychaete species. Significantly higher gene abundances of heterotrophs and mixotrophs were found at the vegetated sites, which could be explained by the finer sediments and short supply of dissolved inorganic nitrogen, respectively. The pigmented protists were more abundant in 18S rRNA gene copies at the lower and higher pH levels than at the intermediate. Nevertheless, the fractions of heterotrophs and phototrophs in the community were significantly related to porewater N:P ratio. These results indicate that seagrass colonization significantly induces an increase in overall biomass and a decrease in diversity of benthic microeukaryotes, making them more heterotrophic. This study also highlights that the hotspot of eukaryotic parasites could be linked with the high productivity of a natural ecosystem.
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Affiliation(s)
- Ying Pan
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Guihao Li
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Lei Su
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Pengfei Zheng
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Yaping Wang
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhuo Shen
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Qiuying Han
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya, China
| | - Jun Gong
- Laboratory of Microbial Ecology and Matter Cycle, School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, China
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Kumar U, Saqib HSA, Islam W, Prashant P, Patel N, Chen W, Yang F, You M, He W. Landscape Composition and Soil Physical-Chemical Properties Drive the Assemblages of Bacteria and Fungi in Conventional Vegetable Fields. Microorganisms 2022; 10:1202. [PMID: 35744721 DOI: 10.3390/microorganisms10061202] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
The soil microbiome is crucial for improving the services and functioning of agroecosystems. Numerous studies have demonstrated the potential of soil physical–chemical properties in driving the belowground microbial assemblages in different agroecosystems. However, not much is known about the assemblage of bacteria and fungi in response to soil physical–chemical properties and the surrounding landscape composition in different vegetable fields of a highly intensive agricultural system. Here, we investigated the effects of soil physical–chemical properties and landscape composition on the community trends of bacteria and fungi in two different soil compartments (bulk and rhizospheric soils) of two different brassica crop types (Chinese cabbage and flower cabbage). The results revealed that bulk soil had a higher alpha diversity of both bacteria and fungi than rhizospheric soil. Each of the soil physical–chemical properties and landscape compositions contributed differently to driving the community structure of distinct bacterial and fungal taxa in both soil compartments and crop types. The higher proportions of forest, grassland, and cultivated land, along with the higher amount of soil calcium in flower cabbage fields, promote the assemblage of Gammaproteobacteria, Actinobacteria, Oxyophotobacteria, Agaricomycetes, and Eurotiomycetes. On the other hand, in Chinese cabbage fields, the increased amounts of iron, zinc, and manganese in the soil together with higher proportions of non-brassica crops in the surrounding landscape strongly support the assemblage of Deltaproteobacteria, Gemmatimonadetes, Bacilli, Clostridia, Alphaproteobacteria, an unknown bacterial species Subgroup-6, Mortierellomycetes, Rhizophlyctidomycetes, and Chytridiomycetes. The findings of this study provide the most comprehensive, comparative, and novel insights related to the bacterial and fungal responses in a highly intensive vegetable growing system for the improvement of the soil fertility and structure. These are important clues for the identification of key bacteria and fungi contributing to the plant–environment interactions and are of a practical significance for landscape-based ecological pest management.
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50
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Zhao L, Nielsen R, Korneliussen TS. distAngsd: Fast and accurate inference of genetic distances for Next Generation Sequencing data. Mol Biol Evol 2022; 39:6596627. [PMID: 35647675 PMCID: PMC9234764 DOI: 10.1093/molbev/msac119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Commonly used methods for inferring phylogenies were designed before the emergence of high throughput sequencing and can generally not accommodate the challenges associated with noisy, diploid sequencing data. In many applications, diploid genomes are still treated as haploid through the use of ambiguity characters; while the uncertainty in genotype calling - arising as a consequence of the sequencing technology - is ignored. In order to address this problem we describe two new probabilistic approaches for estimating genetic distances: distAngsd-geno and distAngsd-nuc, both implemented in a software suite named distAngsd. These methods are specifically designed for next generation sequencing data, utilize the full information from the data, and take uncertainty in genotype calling into account. Through extensive simulations, we show that these new methods are markedly more accurate and have more stable statistical behaviors than other currently available methods for estimating genetic distances - even for very low depth data with high error rates.
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Affiliation(s)
- Lei Zhao
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K
| | - Rasmus Nielsen
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K.,Departments of Integrative Biology and Statistics 3040 Valley Life Sciences Building 3140 Berkeley, CA 94720-3140
| | - Thorfinn Sand Korneliussen
- Section for Geogenetics, Globe Institute, University of Copenhagen, Oster Voldgade 5-7, 1350 Kobenhavn K
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