1
|
Abay M, Abay S, Müştak HK, Diker KS, Gümüşsoy KS, Satıcıoğlu İB, Aydın F. Investigation of Aliarcobacter spp. and Campylobacter spp. in uterine contents of cows: Antibacterial susceptibility and phylogenetic analysis of the isolates. Microb Pathog 2024; 194:106810. [PMID: 39029598 DOI: 10.1016/j.micpath.2024.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/09/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
The study aimed to isolate and identify Aliarcobacter spp. and Campylobacter spp. from the uterine contents of cows and to determine the susceptibilities of the isolates to various antibiotics. For this purpose, a total of 63 cows (with repeat breeder, metritis, and healthy) uterine contents were collected from a slaughterhouse. Pre-enrichment and membrane filtration methods were used to isolate Aliarcobacter and Campylobacter spp., and phenotypic and molecular methods were used to identify the isolates. Antibacterial susceptibilities of the isolates were determined by the disc diffusion method. A total of 11 (17.46 %, 11/63) samples were found positive for both genera, and 12 isolates were obtained from these samples. Out of 9 Campylobacter isolates, 5, 3, and 1 were identified as C. jejuni, C. sputorum, and C. hyointestinalis, respectively. Also, two and one of Aliarcobacter spp. isolates were identified as Aliarcobacter sp. and A. butzleri, respectively. All isolates of both genera were found to be sensitive to amoxicillin-clavulanic acid, ampicillin, erythromycin, and enrofloxacin and resistant to trimethoprim + sulfamethoxazole. This is the first study that reported on the isolation of C. hyointestinalis from cattle uterine contents. It was concluded that Campylobacter and Aliarcobacter species should be considered among the most important etiological agents in uterine infections that cause infertility in cows. The isolation of Aliarcobacter and Campylobacter spp. from healthy cow uteri within the scope of this study suggests the possibility that these agents could colonize the uterus, similar to the colonization observed in the intestine and gallbladder.
Collapse
Affiliation(s)
- Murat Abay
- Erciyes University, Faculty of Veterinary Medicine, Department of Obstetrics and Gynecology, TR-38280, Kayseri, Turkey
| | - Seçil Abay
- Erciyes University, Faculty of Veterinary Medicine, Department of Microbiology, TR-38280, Kayseri, Turkey.
| | - Hamit Kaan Müştak
- Ankara University, Faculty of Veterinary Medicine, Department of Microbiology, TR-06070, Ankara, Turkey
| | - Kadir Serdar Diker
- Aydın Adnan Menderes University, Faculty of Veterinary Medicine, Department of Microbiology, TR-09020, Aydın, Turkey
| | - Kadir Semih Gümüşsoy
- Erciyes University, Faculty of Veterinary Medicine, Department of Microbiology, TR-38280, Kayseri, Turkey; Erciyes Technopark Co., Sistem Veterinary Laboratory Services Ltd., TR-38039, Kayseri, Turkey
| | - İzzet Burçin Satıcıoğlu
- Uludağ University, Faculty of Veterinary Medicine, Department of Aquatic Animal Diseases, TR-16059, Bursa, Turkey
| | - Fuat Aydın
- Erciyes University, Faculty of Veterinary Medicine, Department of Microbiology, TR-38280, Kayseri, Turkey
| |
Collapse
|
2
|
Xi O, Zhang S, Li J, Hu H, Bai M. Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea ( Diglyphus and Pachyneuron) at Various Elevations. INSECTS 2024; 15:497. [PMID: 39057230 PMCID: PMC11277471 DOI: 10.3390/insects15070497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024]
Abstract
Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.
Collapse
Affiliation(s)
- Ouyan Xi
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Shuli Zhang
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Jinzhe Li
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Hongying Hu
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (O.X.); (S.Z.); (J.L.)
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, Urumqi 830017, China
| | - Ming Bai
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100864, China;
| |
Collapse
|
3
|
Allison PF, Pickich ET, Barnett ZC, Garrick RC. DNA barcoding is currently unreliable for species identification in most crayfishes. Ecol Evol 2024; 14:e70050. [PMID: 39041008 PMCID: PMC11260883 DOI: 10.1002/ece3.70050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.
Collapse
Affiliation(s)
| | - Emily T. Pickich
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| | - Zanethia C. Barnett
- Southern Research StationUSDA Forest Service, Center for Bottomland Hardwoods ResearchClemsonSouth CarolinaUSA
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiUniversityMississippiUSA
| |
Collapse
|
4
|
Siddika MA, Ahmed KA, Alam MS, Bushra J, Begum RA. Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama. Sci Rep 2024; 14:13820. [PMID: 38879694 PMCID: PMC11180200 DOI: 10.1038/s41598-024-64791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024] Open
Abstract
The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.
Collapse
Affiliation(s)
- Most Ayesha Siddika
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Mohammad Shamimul Alam
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Jannatul Bushra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Rowshan Ara Begum
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| |
Collapse
|
5
|
Poorrashidi M, Hitchcock M, Xu J. Meta-analyses of the global multilocus genotypes of the human pathogen Campylobacter jejuni. Genome 2024; 67:189-203. [PMID: 38427983 DOI: 10.1139/gen-2023-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Campylobacter infections are a leading cause of bacterial diarrheal illness worldwide, with increasing reports of outbreaks in both developing and developed countries. Most studies investigating strain genotypes and epidemiology of Campylobacter jejuni examined on a local scale. Using the archived multilocus sequence typing data at seven loci, and associated strain metadata from the PubMLST database, here we investigated the spatial and temporal genetic structure of the global population of C. jejuni. Our analyses revealed evidence for clonal dispersals of multiple sequence types (STs) among countries and continents. However, despite the observed clonal dispersal and that most genetic variations were found within individual geographic subpopulations, both the non-clone-corrected and clone-corrected samples showed evidence of significant genetic differentiation among national and continental subpopulations, with non-clone-corrected samples showing greater differentiation than clone-corrected samples. Phylogenetic incompatibility analyses provided evidence for recombination within each continental subpopulation. However, linkage disequilibrium analyses rejected the hypothesis of random recombination across the samples. Temporally, multiple STs were found to persist across four decades and the five globally most common STs showed relatively stable frequencies over the last two decades. We discussed the implications of our results to food security, disease transmission, and public health management.
Collapse
Affiliation(s)
- Monir Poorrashidi
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Megan Hitchcock
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| |
Collapse
|
6
|
Khosravi G, Akbarzadeh K, Karimian F, Koosha M, Saeedi S, Oshaghi MA. A survey of Wolbachia infection in brachyceran flies from Iran. PLoS One 2024; 19:e0301274. [PMID: 38776328 PMCID: PMC11111063 DOI: 10.1371/journal.pone.0301274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/13/2024] [Indexed: 05/24/2024] Open
Abstract
Wolbachia is a maternally inherited intracellular bacterium that is considered to be the most plentiful endosymbiont found in arthropods. It reproductively manipulates its host to increase the chances of being transmitted to the insect progeny; and it is currently used as a means of suppressing disease vector populations or controlling vector-borne diseases. Studies of the dissemination and prevalence of Wolbachia among its arthropod hosts are important for its possible use as a biological control agent. The molecular identification of Wolbachia relies on different primers sets due to Wolbachia strain variation. Here, we screened for the presence of Wolbachia in a broad range of Brachycera fly species (Diptera), collected from different regions of Iran, using nine genetic markers (wsp, ftsZ, fbpA, gatB, CoxA, gltA, GroEL dnaA, and 16s rRNA), for detecting, assessing the sensitivity of primers for detection, and phylogeny of this bacterium. The overall incidence of Wolbachia among 22 species from six families was 27.3%. The most commonly positive fly species were Pollenia sp. and Hydrotaea armipes. However, the bacterium was not found in the most medically important flies or in potential human disease vectors, including Musca domestica, Sarcophaga spp., Calliphora vicinia, Lucilia sericata, and Chrysomya albiceps. The primer sets of 16s rRNA with 53.0% and gatB with 52.0% were the most sensitive primers for detecting Wolbachia. Blast search, phylogenetic, and MLST analysis of the different locus sequences of Wolbachia show that all the six distantly related fly species likely belonging to supergroup A. Our study showed some primer sets generated false negatives in many of the samples, emphasizing the importance of using different loci in detecting Wolbachia. The study provides the groundwork for future studies of a Wolbachia-based program for control of flies.
Collapse
Affiliation(s)
- Ghazal Khosravi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Kamran Akbarzadeh
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Fateh Karimian
- Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Koosha
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahin Saeedi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oshaghi
- Department of Vector Biology and Control of Diseases, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
7
|
Carroll RA, Rice ES, Murphy WJ, Lyons LA, Thibaud-Nissen F, Coghill LM, Swanson WF, Terio KA, Boyd T, Warren WC. A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 2024; 14:8073. [PMID: 38580653 PMCID: PMC10997796 DOI: 10.1038/s41598-024-56003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024] Open
Abstract
The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.
Collapse
Affiliation(s)
- Rachel A Carroll
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX, 77843-4458, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon M Coghill
- Bioinformatics and Analytics Core, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William F Swanson
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, 3400 Vine St., Cincinnati, OH, 45220, USA
| | - Karen A Terio
- Zoological Pathology Program, University of Illinois, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Tyler Boyd
- Oklahoma City Zoo and Botanical Garden, 2000 Remington Pl., Oklahoma, OK, 73111, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
- Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
| |
Collapse
|
8
|
Barnhart E, Kinsey SM, Wright PR, Caldwell SL, Hill V, Kahler A, Mattioli M, Cornman RS, Iwanowicz D, Eddy Z, Halonen S, Mueller R, Peyton BM, Puzon GJ. Naegleria fowleri Detected in Grand Teton National Park Hot Springs. ACS ES&T WATER 2024; 4:628-637. [PMID: 38356928 PMCID: PMC10862551 DOI: 10.1021/acsestwater.3c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024]
Abstract
The free-living thermophilic amoeba Naegleria fowleri (N. fowleri) causes the highly fatal disease primary amoebic meningoencephalitis. The environmental conditions that are favorable to the growth and proliferation of N. fowleri are not well-defined, especially in northern regions of the United States. In this study, we used culture-based methods and multiple molecular approaches to detect and analyzeN. fowleri and other Naegleria spp. in water, sediment, and biofilm samples from five hot spring sites in Grand Teton National Park, Wyoming, U.S.A. These results provide the first detections of N. fowleri in Grand Teton National Park and provide new insights into the distribution of pathogenic N. fowleri and other nonpathogenic Naegleria spp. in natural thermal water systems in northern latitudes.
Collapse
Affiliation(s)
- Elliott
P. Barnhart
- U.S.
Geological Survey, Wyoming/Montana Water Science Center, 3162 Bozeman Ave., Helena, Montana 59601, United States
| | - Stacy M. Kinsey
- U.S.
Geological Survey, Wyoming/Montana Water Science Center, 3162 Bozeman Ave., Helena, Montana 59601, United States
| | - Peter R. Wright
- U.S.
Geological Survey, Wyoming/Montana Water Science Center, 3162 Bozeman Ave., Helena, Montana 59601, United States
| | - Sara L. Caldwell
- U.S.
Geological Survey, Wyoming/Montana Water Science Center, 3162 Bozeman Ave., Helena, Montana 59601, United States
| | - Vince Hill
- U.S.
Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia 30333, United States
| | - Amy Kahler
- U.S.
Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia 30333, United States
| | - Mia Mattioli
- U.S.
Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, Georgia 30333, United States
| | - Robert S. Cornman
- U.S.
Geological Survey, Fort Collins Science Center, 2150 Centre Ave., Bldg. C, Fort Collins, Colorado 80526, United States
| | - Deborah Iwanowicz
- U.S.
Geological Survey, Eastern Ecological Science Center, 11649 Leetown Road, Kearneysville, West Virginia 25430, United States
| | - Zachary Eddy
- U.S.
Geological Survey, Wyoming/Montana Water Science Center, 3162 Bozeman Ave., Helena, Montana 59601, United States
| | - Sandra Halonen
- Department
of Microbiology & Cell Biology, Montana
State University, P.O. Box 173520, Bozeman, Montana 59717, United States
| | - Rebecca Mueller
- Western Regional
Research Center, U.S. Department of Agriculture
Agricultural Research Service, 800 Buchanan St., Albany, California 94710, United States
| | - Brent M. Peyton
- Center
for Biofilm Engineering, Chemical and Biochemical Engineering Department, Montana State University, 366 Barnard Hall, Bozeman Montana 59717, United States
| | - Geoffrey J Puzon
- CSIRO
Environment, Private
Bag No. 5, Wembley, Western
Australia 6913, Australia
| |
Collapse
|
9
|
Pengproh R, Thanyasiriwat T, Sangdee K, Saengprajak J, Kawicha P, Sangdee A. Evaluation and Genome Mining of Bacillus stercoris Isolate B.PNR1 as Potential Agent for Fusarium Wilt Control and Growth Promotion of Tomato. THE PLANT PATHOLOGY JOURNAL 2023; 39:430-448. [PMID: 37817491 PMCID: PMC10580056 DOI: 10.5423/ppj.oa.01.2023.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 08/07/2023] [Accepted: 08/26/2023] [Indexed: 10/12/2023]
Abstract
Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.
Collapse
Affiliation(s)
- Rattana Pengproh
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Thanwanit Thanyasiriwat
- Plant Genome and Disease Research Unit, Department of Agriculture and Resources, Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
| | - Kusavadee Sangdee
- Preclinical Group, Faculty of Medicine, Mahasarakham University, Muang District, Maha Sarakham 44000, Thailand
| | - Juthaporn Saengprajak
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
| | - Praphat Kawicha
- Plant Genome and Disease Research Unit, Department of Agriculture and Resources, Faculty of Natural Resources and Agro-Industry, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand
| | - Aphidech Sangdee
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham 44150, Thailand
- Microbiology and Applied Microbiology Research Unit, Faculty of Science, Mahasarakham University, Kantarawichai District, Maha Sarakham 44150, Thailand
| |
Collapse
|
10
|
Riza LS, Zain MI, Izzuddin A, Prasetyo Y, Hidayat T, Abu Samah KAF. Implementation of machine learning in DNA barcoding for determining the plant family taxonomy. Heliyon 2023; 9:e20161. [PMID: 37767518 PMCID: PMC10520734 DOI: 10.1016/j.heliyon.2023.e20161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The DNA barcoding approach has been used extensively in taxonomy and phylogenetics. The differences in certain DNA sequences are able to differentiate and help classify organisms into taxa. It has been used in cases of taxonomic disputes where morphology by itself is insufficient. This research aimed to utilize hierarchical clustering, an unsupervised machine learning method, to determine and resolve disputes in plant family taxonomy. We take a case study of Leguminosae that historically some classify into three families (Fabaceae, Caesalpiniaceae, and Mimosaceae) but others classify into one family (Leguminosae). This study is divided into several phases, which are: (i) data collection, (ii) data preprocessing, (iii) finding the best distance method, and (iv) determining disputed family. The data used are collected from several sources, including National Center for Biotechnology Information (NCBI), journals, and websites. The data for validation of the methods were collected from NCBI. This was used to determine the best distance method for differentiating families or genera. The data for the case study in the Leguminosae group was collected from journals and a website. From the experiment that we have conducted, we found that the Pearson method is the best distance method to do clustering ITS sequence of plants, both in accuracy and computational cost. We use the Pearson method to determine the disputed family between Leguminosae. We found that the case study of Leguminosae should be grouped into one family based on our research.
Collapse
Affiliation(s)
- Lala Septem Riza
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Muhammad Iqbal Zain
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Ahmad Izzuddin
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Yudi Prasetyo
- Department of Computer Science Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Topik Hidayat
- Department of Biology Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | | |
Collapse
|
11
|
Li H, Jiang Z, Zhou J, Liu X, Zhang Y, Chu D. Ecological Factors Associated with the Distribution of Bemisia tabaci Cryptic Species and Their Facultative Endosymbionts. INSECTS 2023; 14:252. [PMID: 36975937 PMCID: PMC10053707 DOI: 10.3390/insects14030252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The sweetpotato whitefly, Bemisia tabaci species complex, comprises at least 44 morphologically indistinguishable cryptic species, whose endosymbiont infection patterns often varied at the spatial and temporal dimension. However, the effects of ecological factors (e.g., climatic or geographical factors) on the distribution of whitefly and the infection frequencies of their endosymbionts have not been fully elucidated. We, here, analyzed the associations between ecological factors and the distribution of whitefly and their three facultative endosymbionts (Candidatus Cardinium hertigii, Candidatus Hamiltonella defensa, and Rickettsia sp.) by screening 665 individuals collected from 29 geographical localities across China. The study identified eight B. tabaci species via mitochondrial cytochrome oxidase I (mtCOI) gene sequence alignment: two invasive species, MED (66.9%) and MEAM1 (12.2%), and six native cryptic species (20.9%), which differed in distribution patterns, ecological niches, and high suitability areas. The infection frequencies of the three endosymbionts in different cryptic species were distinct and multiple infections were relatively common in B. tabaci MED populations. Furthermore, the annual mean temperature positively affected Cardinium sp. and Rickettsia sp. infection frequencies in B. tabaci MED but negatively affected the quantitative distribution of B. tabaci MED, which indicates that Cardinium sp. and Rickettsia sp. maybe play a crucial role in the thermotolerance of B. tabaci MED, although the host whitefly per se exhibits no resistance to high temperature. Our findings revealed the complex effects of ecological factors on the expansion of the invasive whitefly.
Collapse
Affiliation(s)
- Hongran Li
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 515100, China
| | - Zhihui Jiang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Jincheng Zhou
- Department of Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xin Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, College of Agriculture, Henan University, Kaifeng 475004, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Chu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| |
Collapse
|
12
|
Saticioglu IB, Ay H, Altun S, Karakaya E, Gunduz ES, Aydogdu D, Yarim D, Erkek N, Duman M. Genomic insight into Myroides oncorhynchi sp. nov., a new member of the Myroides genus, isolated from the internal organ of rainbow trout (Oncorhynchus mykiss). Antonie Van Leeuwenhoek 2023; 116:291-302. [PMID: 36586048 DOI: 10.1007/s10482-022-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023]
Abstract
The strain M-43T was isolated from the Oncorhynchus mykiss from a fish farm in Mugla, Turkey. Pairwise 16S rRNA gene sequence analysis was used to identify strain M-43T. The strain was a member of the genus Myroides sharing the highest 16S rRNA gene sequence identity levels of 98.7%, 98.3%, and 98.3% with the type strains of M. profundi D25T, M. odoratimimus subsp. odoratimimus CCUG 39352T and M. odoratimimus subsp. xuanwuensis DSM27251T, respectively. A polyphasic taxonomic approach including whole genome-based analyses was employed to confirm the taxonomic provenance of strain M-43T within the genus Myroides. The overall genome relatedness indices (OGRI) for strain M-43T compared with its most closely related type strains M. odoratimimus subsp. xuanwuensis DSM 27251T, M. profundi D25T, and M. odoratimimus subsp. odoratimimus ATCC BAA-634T, were calculated as 25.3%, 25.1%, and 25% for digital DNA-DNA hybridization (dDDH), 83.3%, 83.6%, and 83.4% for average nucleotide identity (ANI) analyses, respectively. The OGRI values between strain M-43T and its close neighbors confirmed that the strain represents a novel species in the genus Myroides. The DNA G + C content of the strain is 33.7%. The major fatty acids are iso-C15:0 and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0). The predominant polar lipids are phosphatidylethanolamine, an amino-lipid and five unidentified lipids. The major respiratory quinone is MK-6. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name Myroides oncorhynchi sp. nov. is proposed, with M-43T as the type strain (JCM 34205T = KCTC 82265T).
Collapse
Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, 55139, Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Enes Said Gunduz
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Duygu Aydogdu
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Dogancan Yarim
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Neslihan Erkek
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| |
Collapse
|
13
|
Wang H, Lu Y, Zhang T, Liu Z, Cao L, Chang Q, Liu Y, Lu X, Yu S, Li H, Jiang J, Liu G, Sederoff HW, Sederoff RR, Zhang Q, Zheng Z. The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion. PLANT PHYSIOLOGY 2023; 191:1122-1137. [PMID: 36494195 PMCID: PMC9922402 DOI: 10.1093/plphys/kiac571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
As essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through bovine serum albumin sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.
Collapse
|
14
|
Saticioglu IB, Ay H, Altun S, Duman M. Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2023; 46:126385. [PMID: 36410095 DOI: 10.1016/j.syapm.2022.126385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
Collapse
Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey; Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| |
Collapse
|
15
|
Siles JA, Hendrickson AJ, Terry N. Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 322:116132. [PMID: 36067666 DOI: 10.1016/j.jenvman.2022.116132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.
Collapse
Affiliation(s)
- José A Siles
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA.
| | - Andrew J Hendrickson
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Norman Terry
- Department of Plant & Microbial Biology, University of California at Berkeley, Berkeley, CA, 94720, USA
| |
Collapse
|
16
|
A dataset representing the identification of three microalgae species isolated from freshwater areas at Glami Lemi River, Malaysia. Data Brief 2022; 45:108761. [DOI: 10.1016/j.dib.2022.108761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
|
17
|
Liu Y, Cui X, Yang R, Zhang Y, Xu Y, Liu G, Zhang B, Wang J, Wang X, Zhang W, Chen T, Zhang G. Genomic Insights into the Radiation-Resistant Capability of Sphingomonas qomolangmaensis S5-59 T and Sphingomonas glaciei S8-45 T, Two Novel Bacteria from the North Slope of Mount Everest. Microorganisms 2022; 10:microorganisms10102037. [PMID: 36296313 PMCID: PMC9611098 DOI: 10.3390/microorganisms10102037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Mount Everest provides natural advantages to finding radiation-resistant extremophiles that are functionally mechanistic and possess commercial significance. (1) Background: Two bacterial strains, designated S5-59T and S8-45T, were isolated from moraine samples collected from the north slope of Mount Everest at altitudes of 5700m and 5100m above sea level. (2) Methods: The present study investigated the polyphasic features and genomic characteristics of S5-59T and S8-45T. (3) Results: The major fatty acids and the predominant respiratory menaquinone of S5-59T and S8-45T were summed as feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c) and ubiquinone-10 (Q-10). Phylogenetic analyses based on 16S rRNA sequences and average nucleotide identity values among these two strains and their reference type strains were below the species demarcation thresholds of 98.65% and 95%. Strains S5-59T and S8-45T harbored great radiation resistance. The genomic analyses showed that DNA damage repair genes, such as mutL, mutS, radA, radC, recF, recN, etc., were present in the S5-59T and S8-45T strains. Additionally, strain S5-59T possessed more genes related to DNA protection proteins. The pan-genome analysis and horizontal gene transfers revealed that strains of Sphingomonas had a consistently homologous genetic evolutionary radiation resistance. Moreover, enzymatic antioxidative proteins also served critical roles in converting ROS into harmless molecules that resulted in resistance to radiation. Further, pigments and carotenoids such as zeaxanthin and alkylresorcinols of the non-enzymatic antioxidative system were also predicted to protect them from radiation. (4) Conclusions: Type strains S5-59T (=JCM 35564T =GDMCC 1.3193T) and S8-45T (=JCM 34749T =GDMCC 1.2715T) represent two novel species of the genus Sphingomonas with the proposed name Sphingomonas qomolangmaensis sp. nov. and Sphingomonas glaciei sp. nov. The type strains, S5-59T and S8-45T, were assessed in a deeply genomic study of their radiation-resistant mechanisms and this thus resulted in a further understanding of their greater potential application for the development of anti-radiation protective drugs.
Collapse
Affiliation(s)
- Yang Liu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, China
| | - Yiyang Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yeteng Xu
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Stomatology, Lanzhou University, Lanzhou 730000, China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Jinxiu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Xinyue Wang
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Correspondence: (T.C.); (G.Z.)
| |
Collapse
|
18
|
Alamil M, Thébaud G, Berthier K, Soubeyrand S. Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics. Front Microbiol 2022; 13:983938. [PMID: 36274731 PMCID: PMC9581327 DOI: 10.3389/fmicb.2022.983938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial communities and to infer transmission links in infectious disease outbreaks. The performance of such characterizations and inferences cannot be analytically assessed in general and are often grounded on computer-intensive evaluations. Then, being able to simulate within-host genetic diversity across time under various demo-genetic assumptions is paramount to assess the performance of the approaches of interest. In this context, we built an original model that can be simulated to investigate the temporal evolution of genotypes and their frequencies under various demo-genetic assumptions. The model describes the growth and the mutation of genotypes at the nucleotide resolution conditional on an overall within-host viral kinetics, and can be tuned to generate fast non-equilibrium demo-genetic dynamics. We ran simulations of this model and computed classic diversity indices to characterize the temporal variation of within-host genetic diversity (from high-throughput amplicon sequences) of virus populations under three demographic kinetic models of viral infection. Our results highlight how demographic (viral load) and genetic (mutation, selection, or drift) factors drive variations in within-host diversity during the course of an infection. In particular, we observed a non-monotonic relationship between pathogen population size and genetic diversity, and a reduction of the impact of mutation on diversity when a non-specific host immune response is activated. The large variation in the diversity patterns generated in our simulations suggests that the underlying model provides a flexible basis to produce very diverse demo-genetic scenarios and test, for instance, methods for the inference of transmission links during outbreaks.
Collapse
Affiliation(s)
- Maryam Alamil
- INRAE, BioSP, Avignon, France
- Department of Mathematics and Computer Science, Alfaisal University, Riyadh, Saudi Arabia
- *Correspondence: Maryam Alamil ;
| | - Gaël Thébaud
- PHIM Plant Health Institute, INRAE, Univ Montpellier, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | | |
Collapse
|
19
|
Cui X, Liu Y, Xu Y, Chen T, Zhang S, Wang J, Yang R, Liu G, Zhang W, Zhang G. Paracoccus everestensis sp. nov., a novel bacterium with great antioxidant capacity isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S8-55T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus
Paracoccus
, and explore the antioxidant capacity of strain S8-55T. The polyphasic study confirmed the affiliation of strain S8-55T with the genus
Paracoccus
. Strain S8-55T was aerobic, Gram-negative and oxidase- and catalase positive. Cells were orange-pigmented, ellipsoid and had no spore formation, no flagella and no motility. Strain S8-55T grow at 10–37 °C, pH 7–11 and without NaCl. Ubiquinone 10 was its predominant respiratory menaquinone. The polar lipids of strain S8-55T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and three unidentified lipids. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The G+C content was 64.3 mol%. The phylogenetic analysis based on the 16S rRNA sequence showed that strain S8-55T was closely related to
Paracoccus angustae
E6T (97.9 %),
Paracoccus aerius
011410T (97.9 %) and
Paracoccus hibisci
THG-T2.8T (97.8 %). The average nucleotide identity values among strain S8-55T and
P. angustae
CCTCC AB 2015056T,
P. aerius
KCTC 42845T and
P. hibisci
CCTCC AB 2016181T were 84.1, 84.5 and 76.3 %, respectively. The genome of strain S8-55T contained antioxidant genes such as oxyR, recD, katE, recD and rpoH. Based on its morphological, physiological and chemical taxonomic characteristics, strain S8-55T (=JCM 35 227T=GDMCC 1.3026T) should be classified as a novel species of the genus
Paracoccus
with the proposed name Paracoccus everestensis sp. nov.
Collapse
Affiliation(s)
- Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Yajie Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Songlin Zhang
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Jinxiu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, Gansu Province, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| |
Collapse
|
20
|
Schick LA, Wohlsein P, Rautenschlein S, Jung A, Boyi JO, Glemarec G, Kroner AM, Barth SA, Siebert U. Health Status of Bycaught Common Eiders (Somateria mollissima) from the Western Baltic Sea. Animals (Basel) 2022; 12:ani12152002. [PMID: 35953991 PMCID: PMC9367620 DOI: 10.3390/ani12152002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 01/21/2023] Open
Abstract
Simple Summary We performed post-mortem investigations of 121 Common Eiders (Somateria mollissima), which were incidentally caught in fishing gear from 2017 to 2019 in Denmark. The aim of the study was to obtain an overview of health issues and pathogens occurring in the population of these birds. The European population of the Common Eider is endangered, but the reasons for the decline of the population have not yet been determined. In times of accelerating species loss, it is important to determine factors that impact population numbers of declining species. The post-mortem investigations included biometric measurements and determination of age, sex and nutritional status, as well as parasitological, bacteriological and virological investigations. The majority of Common Eiders had a good or moderate nutritional status. Most animals were infected with intestinal parasites, and we commonly found inflammation in organs like the liver, kidneys, intestine and the oesophagus. In three animals, a pathogenic bacterium caused inflammatory lesions in several organs. We did not find signs for epizootic diseases or pathologies, which would explain the declining species numbers. Abstract The Common Eider (Somateria mollissima) inhabits the entire northern hemisphere. In northern Europe, the flyway population reaches from the southern Wadden Sea to the northern Baltic coast. The European population is classified as endangered due to declines in Common Eider numbers across Europe since 1990. In this study, we assessed 121 carcasses of Common Eiders, captured incidentally in gillnets in the Western Baltic between 2017 and 2019. The most common findings were parasitic infections of the intestine by acanthocephalans in 95 animals, which correlated with enteritis in 50% of the cases. Parasites were identified as Profilicollis botulus in 25 selected animals. Additionally, oesophageal pustules, erosions, and ulcerations, presumably of traumatic origin, were frequently observed. Nephritis and hepatitis were frequent, but could not be attributed to specific causes. Lung oedema, fractures and subcutaneous haemorrhages likely resulted from entangling and drowning. Two Common Eiders had mycobacterial infections and in one of these, Mycobacterium avium subspecies (ssp.) avium was identified. This study gives an overview of morphological changes and infectious diseases from one location of the European flyway population. It contributes to future health studies on Common Eiders in the Baltic and Wadden Seas by providing baseline information to compare with other areas or circumstances.
Collapse
Affiliation(s)
- Luca A. Schick
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstraße 6, 25761 Büsum, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Silke Rautenschlein
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559 Hannover, Germany
| | - Joy Ometere Boyi
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstraße 6, 25761 Büsum, Germany
| | - Gildas Glemarec
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Anne-Mette Kroner
- National Institute of Aquatic Resources, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Stefanie A. Barth
- Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Werftstraße 6, 25761 Büsum, Germany
- Correspondence: ; Tel.: +49-511-856-8158
| |
Collapse
|
21
|
Altun S, Duman M, Ay H, Saticioglu IB. Shewanella oncorhynchi sp. nov., a novel member of the genus Shewanella, isolated from Rainbow Trout (Oncorhynchus mykiss). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A strain, S-1T was isolated from rainbow trout (Oncorhynchus mykiss) exhibiting clinical symptoms of lens atrophy, inappetence, visual impairment and growth retardation. The strain was identified as representing a member of the genus
Shewanella
on the basis of the results of 16S rRNA gene sequence analysis. The neighbor-joining phylogenetic tree based on 16S rRNA gene sequences indicated that S-1T clustered with
Shewanella putrefaciens
JCM 20190T,
Shewanella profunda
DSM 15900T, and
Shewanella hafniensis
P010T, sharing 99.3, 98.8 and 87.7% 16S rRNA gene similarities, respectively. A polyphasic taxonomic approach including phenotypic, chemotaxonomic, and genomic characterization was employed to ascertain the taxonomic position of S-1T within the genus
Shewanella
. The overall genome relatedness indices (OGRI) for S-1T compared with the most closely related type strains
S. hafniensis
ATCC BAA-1207T,
Shewanella baltica
NCTC 10735T,
S. putrefaciens
ATCC 8071T and
S. profunda
DSM 15900T were calculated as 40.8, 40.1, 28.5 and 27.3% for digital DNA–DNA hybridization (dDDH), and 91.6, 91.0, 86.3 and 85.1% for average nucleotide identity (ANI), respectively. OGRI values between S-1T and its close neighbours confirmed that the strain represents a novel species in the genus
Shewanella
.The DNA G+C content of the strain is 45.2%. Major fatty acids were C17 : 1ω8c, C15 : 0iso, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant polar lipids were phosphatidylethanolamine, phospholipid, amino-phospholipid and unidentified lipids. The major respiratory quinones were ubiquinone-8, ubiquinone-7 and menaquinone-7. Chemotaxonomic and phylogenomic analyses of this isolate confirmed that the strain represents a novel species for which the name
Shewanella oncorhynchi
sp. nov. is proposed, with S-1T as the type strain (JCM 34183T= KCTC 82249T).
Collapse
Affiliation(s)
- Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, 16059, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, 55139, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, Kayseri 38280, Turkey
- Present address: Keles Vocational School, Bursa Uludag University, Bursa, 16059, Turkey
| |
Collapse
|
22
|
Aydin F, Karakaya E, Kayman T, Abay S, Saticioglu IB. Helicobacter turcicus sp. nov., a catalase-negative new member of the Helicobacter genus, isolated from Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven Gram-negative, curved and S-shaped, oxidase activity positive, catalase activity negative bacterial isolates recovered from faeces of Anatolian ground squirrel (Spermophilus xanthoprymnus) in the city of Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR revealed that these isolates belonged to the genus
Helicobacter
. The 16S rRNA gene sequence analysis revealed that the 11 isolates had over 99 % sequence identity with each other and were most closely related to
Helicobacter ganmani
CMRI H02T with 97.0–97.1 % identity levels and they formed a novel phylogenetic line within the genus
Helicobacter
. Faydin-H64 and Faydin-H70T strains were subjected to gyrA and atpA gene and whole genome sequence analyses. These two
Helicobacter
strains formed separate phylogenetic clades, divergent from other known
Helicobacter
species. The DNA G+C content and genome size of the strain Faydin-H70T were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Faydin-H70T and its close phylogenetic neighbour H. winghamensis ATCC BAA-430T were determined as 81.7 and 34.9 %, respectively. Pairwise sequence comparison showed that it was closely related to
H. ganmani
CMRI H02T however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430T. The data obtained from the polyphasic taxonomy approach, including phenotypic characterization and whole-genome sequences, revealed that these strains represent a novel species within the genus
Helicobacter
, for which the name Helicobacter turcicus sp. nov., is proposed with Faydin-H70T as the type strain (=DSM 112556T=LMG 32335T).
Collapse
Affiliation(s)
- Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | - Tuba Kayman
- Medical Microbiology Clinic, Şişli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, 34371 Istanbul, Turkey
| | - Secil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
| | | |
Collapse
|
23
|
Aydin F, Saticioglu IB, Ay H, Kayman T, Karakaya E, Abay S. Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds. Syst Appl Microbiol 2022; 45:126326. [DOI: 10.1016/j.syapm.2022.126326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
|
24
|
Liu Y, Chen T, Cui X, Xu Y, Hu S, Zhao Y, Zhang W, Liu G, Zhang G. Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus
Sphingomonas
. Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to
Sphingomonas panaciterrae
DCY91T (98.17 %),
Sphingomonas olei
K-1-16T (98.11 %) and
Sphingomonas mucosissima
DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and
Sphingomonas panaciterrae
DCY91T,
Sphingomonas olei
K-1-16T and
Sphingomonas mucosissima
DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus
Sphingomonas
, for which we propose the name Sphingomonas radiodurans sp. nov.
Collapse
Affiliation(s)
- Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Xiaowen Cui
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yeteng Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Shixin Hu
- Institute of Applied Magnetics, Key Laboratory for Magnetism and Magnetic Materials of the Ministry of Education, Lanzhou University, Lanzhou 730000, PR China
| | - Yidan Zhao
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| |
Collapse
|
25
|
High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. BIOLOGY 2022; 11:biology11040501. [PMID: 35453702 PMCID: PMC9030528 DOI: 10.3390/biology11040501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles. Abstract The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m2 and 6000 J/m2 UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
Collapse
|
26
|
Gadawski P, Montagna M, Rossaro B, Giłka W, Pešić V, Grabowski M, Magoga G. DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Affiliation(s)
- Piotr Gadawski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Matteo Montagna
- Department of Agricultural Sciences University of Naples Federico II Portici Italy
- BAT Center ‐ Interuniversity Center for Studies on Bioinspired Agro‐environmental Technology University of Napoli Federico II Portici Italy
| | - Bruno Rossaro
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
| | - Wojciech Giłka
- Laboratory of Systematic Zoology Department of Invertebrate Zoology and Parasitology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Vladimir Pešić
- Department of Biology Faculty of Science University of Montenegro Podgorica Montenegro
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology University of Lodz Lodz Poland
| | - Giulia Magoga
- Department of Agricultural and Environmental Sciences – Production, Landscape, Agroenergy University of Milan Milan Italy
| |
Collapse
|
27
|
Mislabelled frozen fish fillets in the Klang Valley in Malaysia and its potential impact on consumers. J Verbrauch Lebensm 2022. [DOI: 10.1007/s00003-022-01373-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Ahmad HI, Afzal G, Iqbal MN, Iqbal MA, Shokrollahi B, Mansoor MK, Chen J. Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals. Front Vet Sci 2022; 8:814765. [PMID: 35174241 PMCID: PMC8841730 DOI: 10.3389/fvets.2021.814765] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/24/2021] [Indexed: 12/17/2022] Open
Abstract
The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.
Collapse
Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | | | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Muhammad Khalid Mansoor
- Department of Microbiology, Faculty of Veterinary and Animal Science, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Jinping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Jinping Chen
| |
Collapse
|
29
|
Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates. Virus Res 2022; 307:198618. [PMID: 34740719 PMCID: PMC8563081 DOI: 10.1016/j.virusres.2021.198618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 01/01/2023]
Abstract
The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic variants. Brazil is the world's second-most COVID-19 affected country. In the present study, we identified the genomic and proteomic variants of Brazilian SARS-CoV-2 isolates. We identified 16 different genotypic variants were found among the 27 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2′O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). A mutation in RdRp of SARS-CoV-2, particularly the change of Pro-to Leu-at 323 resulted in the stabilization of the structure in BRA/CD1739-P4/2020. NSP4, NSP5 protein mutants are more virulent in genotype 15 and 16. A fast protein folding rate changes the structural stability and leads to escape for current antivirals. Thus, our findings help researchers to develop the best potent antivirals based on the new mutant of Brazilian isolates.
Collapse
|
30
|
Çelebi Ö, Özdemir Ü, Büyük F, Baca AÜ, Erpek ŞH, Karahan M, Otlu S, Şahin M, Coşkun MR, Çelik E, Sağlam AG, Büyük E, Akça D. Isolation of Mycoplasma spp. from Geese with Pneumonia and Identification of Microbial Isolates via Molecular Methods. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Ü Özdemir
- Pendik Veterinary Control Institute, Turkey
| | | | | | - ŞH Erpek
- Pendik Veterinary Control Institute, Turkey
| | - M Karahan
- Pendik Veterinary Control Institute, Turkey
| | - S Otlu
- Kafkas University, Turkey
| | | | | | | | | | | | - D Akça
- Kafkas University, Turkey
| |
Collapse
|
31
|
A SYBR Green-based real-time RT-PCR assay to differentiate the H1N1 influenza virus lineages. J Virol Methods 2021; 300:114387. [PMID: 34848281 DOI: 10.1016/j.jviromet.2021.114387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2021] [Accepted: 11/25/2021] [Indexed: 12/15/2022]
Abstract
The H1N1 subtype influenza viruses (H1N1) have been causing persistent epidemics in human, swine and poultry populations since 1918. This subtype has evolved into four relatively stable genetic lineages, including classical swine influenza virus lineage, seasonal human influenza virus lineage, avian influenza virus lineage and Eurasian avian-like swine influenza virus lineage. In this study, four pairs of primers, based on the relatively conserved HA nucleotide regions of each H1N1 genetic lineage, were designed to establish a SYBR Green-based real-time quantitative RT-PCR (qPCR) assay to differentiate between the H1N1 genetic lineages. The results of qPCR assay showed that the lineage-specific primers designed for each H1N1 lineage were intra-lineage-specific, without mismatch of inter-lineage or inter-subtype and there appeared specific amplification curves when the concentrations of H1N1 plasmids were greater than or equal to 1.0 × 101 copies/reaction. Thus, this qPCR assay can specifically differentiate between the four lineages of H1N1 with a good specificity and sensitivity, which would assist in recognizing the infection and epidemic status of different H1N1 genetic lineages.
Collapse
|
32
|
Aydin F, Abay S, Kayman T, Karakaya E, Mustak HK, Mustak IB, Bilgen N, Goncuoglu M, Duzler A, Guran O, Sahin O, Saticioglu IB. Campylobacter anatolicus sp. nov., a novel member of the genus Campylobacter isolated from feces of Anatolian Ground Squirrel (Spermophilus xanthoprymnus) in Turkey. Syst Appl Microbiol 2021; 44:126265. [PMID: 34624709 DOI: 10.1016/j.syapm.2021.126265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Seventy-four Gram-negative, motile, slightly curved rod-shaped, microaerophilic, oxidase-positive and catalase-negative isolates, recovered from fecal samples of the Anatolian ground squirrel (Spermophilus xanthoprymnus) in Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that all isolates belonged to the genus Campylobacter. 16S rRNA gene sequence analyses revealed the closest match as Campylobacter curvus DSM 6644T with identity levels of 96.41-96.70%. Based on the 16S rRNA gene phylogeny of the 74 isolates, six isolates (faydin-G24, faydin-G52, faydin-G105, faydin-G114, faydin-G129 and faydin-G140T) were chosen as representatives for further characterization. The overall genome relatedness indices for the strain faydin-G140T, compared to the most closely related type strain C. curvus ATCC 35224T, were calculated as 15.2%, 72.5%, and 83.7% for digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANIb and ANIm), respectively. The G+C content and genome size of the strains ranged between 35.2-35.4 mol% and 1.7-1.8 Mb, respectively. Based on data obtained from the polyphasic taxonomy approach, including phenotypic characterization as well as genomic and chemotaxonomic analyses, these strains are concluded to represent a novel species, for which the name Campylobacter anatolicus sp. nov. is proposed with faydin-G140T as the type strain (=DSM 112311T = LMG 32238T).
Collapse
Affiliation(s)
- Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Secil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Tuba Kayman
- Medical Microbiology Clinic, Şişli Hamidiye Etfal Training and Research Hospital, University of Health Sciences, 34371 Istanbul, Turkey
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Hamit Kaan Mustak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Inci Basak Mustak
- Department of Microbiology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Nuket Bilgen
- Department of Genetics, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Muammer Goncuoglu
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Ayhan Duzler
- Department of Anatomy, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Ozgur Guran
- Faculty of Veterinary Medicine, Ankara University, 06110 Ankara, Turkey
| | - Orhan Sahin
- Department of Veterinary Diagnostic & Production Animal Medicine, College of Veterinary Medicine, Iowa State University, 50011 Ames, Iowa, United States of America
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| |
Collapse
|
33
|
Do T, Inpankaew T, Duong DH, Bui KL. First Molecular Evidence of Pathogens in Fleas Collected from Dogs in Northern Vietnam. Pathogens 2021; 10:pathogens10091185. [PMID: 34578217 PMCID: PMC8472576 DOI: 10.3390/pathogens10091185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 11/16/2022] Open
Abstract
Fleas are considered as hosts for a wide range of pathogens that cause emerging and re-emerging zoonotic diseases worldwide. Data on fleas and flea-borne pathogens (FBPs) in the international literature are limited in Vietnam. This study aimed to investigate the species of fleas and the presence of pathogens of interest in fleas in northern Vietnam using PCR and sequence analysis. Out of 200 dogs enrolled in this study, 20% were infested by the flea species Ctenocephalides felis felis. In total, 62 fleas (35 females and 27 males) collected from domestic dogs were molecularly screened for the detection of pathogens. Out of the screened fleas, 39 were positive for Rickettsia felis (62.9%), 9 for Candidatus Mycoplasma hemobos (14.52%), and 6 for Mycoplasma wenyonii (9.68%). This study shows the first molecular detection of the above-mentioned pathogens in fleas collected from the studied areas and the potential risk of infection with examined FBPs in northern Vietnam.
Collapse
Affiliation(s)
- Thom Do
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (T.D.); (T.I.)
| | - Tawin Inpankaew
- Department of Parasitology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand; (T.D.); (T.I.)
| | - Duc Hieu Duong
- Department of Parasitology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 12406, Vietnam;
| | - Khanh Linh Bui
- Department of Parasitology, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi 12406, Vietnam;
- Correspondence:
| |
Collapse
|
34
|
Li N, Chen S, Yan Z, Han J, Ta Y, Pu T, Wang Y. Antimicrobial Activity and Identification of the Biosynthetic Gene Cluster of X-14952B From Streptomyces sp. 135. Front Microbiol 2021; 12:703093. [PMID: 34408734 PMCID: PMC8365161 DOI: 10.3389/fmicb.2021.703093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 12/03/2022] Open
Abstract
The bacterial genus Streptomyces is an important source of antibiotics, and genome mining is a valuable tool to explore the potential of microbial biosynthesis in members of this genus. This study reports an actinomycete strain 135, which was isolated from Qinghai-Tibet Plateau in China and displayed broad antimicrobial activity. The fermentation broth of strain 135 displayed strong antifungal activity (>70%) against Sclerotinia sclerotiorum, Botrytis cinerea, Valsa mali, Phytophthora capsici, Glomerella cingulata, Magnaporthe grisea, Bipolaris maydis, Exserohilum turcicum in vitro, meanwhile possessed significant preventive and curative efficacy against S. sclerotiorum, Gaeumannomyces graminis, and P. capsici on rape leaves (54.04 and 74.18%), wheat (90.66 and 67.99%), and pepper plants (79.33 and 66.67%). X-14952B showed the greatest antifungal activity against S. sclerotiorum and Fusarium graminearum which the 50% inhibition concentration (EC50) were up to 0.049 and 0.04 μg/mL, respectively. Characterization of strain 135 using a polyphasic approach revealed that the strain displayed typical features of the genus Streptomyces. 16S rRNA gene sequencing and phylogenetic analysis demonstrated that the isolate was most closely related to and formed a clade with Streptomyces huasconensis HST28T (98.96% 16S rRNA gene sequence similarity). Average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values in strain 135 and related type strains were both below the threshold of species determination (91.39 and 56.5%, respectively). OrthoANI values between strain 135 and related type strains are under the cutoff of determining species (<95%). The biosynthetic gene cluster (BGC) designated to X-14952B biosynthesis was identified through genome mining and the possible biosynthesis process was deduced.
Collapse
Affiliation(s)
- Na Li
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China.,Institute Vegetable, Zhangye Academy of Agricultural Sciences, Zhangye, China
| | - Simin Chen
- College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Zhiqiang Yan
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Jinhua Han
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Yongquan Ta
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Taixun Pu
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| | - Yonghong Wang
- Research and Development Center of Biorational Pesticides, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Xianyang, China
| |
Collapse
|
35
|
Khanmohammadi M, Zolfaghari-Emameh R, Arshadi M, Razmjou E, Karimi P. Molecular Identification and Genotyping of Babesia canis in Dogs from Meshkin Shahr County, Northwestern Iran. J Arthropod Borne Dis 2021; 15:97-107. [PMID: 34277859 PMCID: PMC8271237 DOI: 10.18502/jad.v15i1.6489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 03/13/2021] [Indexed: 11/24/2022] Open
Abstract
Background Canine babesiosis is one of the mainly worldwide-distributed tick-borne haemoprotozoan parasitic diseases in dogs. Methods A total of 43 blood samples were randomly collected from naturally infected dogs in seven villages from different geographical areas of Meshkin Shahr, Ardabil Province, Iran. The presence of Babesia species detected with standard methods including parasitological and gene sequencing techniques targeting the 18S rRNA gene. Results Our results revealed that four dogs 9.3% (4/43) including one female and three male dogs were infected with Babesia. All four Babesia-infected dogs were confirmed B. canis by the molecular-based method. Sequence alignments comparison of the B. canis genotypes A and B, it was revealed that all B. canis isolates belonged to genotype B. Conclusion This study provides essential data for subsequently define the critical importance of the molecular studies in management and prevention of the canine babesiosis in Iran.
Collapse
Affiliation(s)
- Majid Khanmohammadi
- Department of Laboratory Sciences, Marand Branch, Islamic Azad University, Marand, Iran
| | - Reza Zolfaghari-Emameh
- Department of Energy and Environmental Biotechnology, Division of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Mehdi Arshadi
- Al-Zahra Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Razmjou
- Department of Medical Parasitology and Mycology, Iran University of Medical Sciences, Tehran, Iran
| | - Poorya Karimi
- Department of Medical Parasitology and Mycology, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
36
|
Kania A, Sarapata K. The robustness of the chaos game representation to mutations and its application in free-alignment methods. Genomics 2021; 113:1428-1437. [PMID: 33713823 DOI: 10.1016/j.ygeno.2021.03.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
Numerical representation of biological sequences plays an important role in bioinformatics and has many practical applications. One of the most popular approaches is the chaos game representation. In this paper, the authors propose a novel look into chaos game construction - an analytical description of this procedure. This type enables to build more general number sequences using different weight functions. The authors suggest three conditions that these functions should hold. Additionally, they present some criteria to compare them and check whether they provide a unique representation. One of the most important advantages of our approach is the possibility to construct such a description that is less sensitive to mutations and as a result, give more reliable values for free-alignment phylogenetic trees constructions. Finally, the authors applied the DFT method using four types of functions and compared the obtained results using the BLAST tool.
Collapse
Affiliation(s)
- Adrian Kania
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland.
| | - Krzysztof Sarapata
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| |
Collapse
|
37
|
Saticioglu IB, Ay H, Altun S, Duman M, Sahin N. Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2021; 44:126186. [PMID: 33647765 DOI: 10.1016/j.syapm.2021.126186] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.
Collapse
Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| |
Collapse
|
38
|
Molecular Identification and Phylogenetic Analysis of the Traditional Chinese Medicinal Plant Kochia scoparia Using ITS2 Barcoding. Interdiscip Sci 2021; 13:128-139. [PMID: 33595803 DOI: 10.1007/s12539-021-00421-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/17/2021] [Accepted: 02/01/2021] [Indexed: 10/22/2022]
Abstract
Kochia scoparia has high medicinal and economic value. However, with similar morphological features, adulterants and some closely related species of K. scoparia are increasingly sold in the medicinal markets, leading to potential safety risks. In this study, 128 internal transcribed spacer 2 (ITS2) sequences were collected to distinguish K. scoparia from its closely related species and adulterants. Then, sequence alignment, sequence characteristics analysis, and genetic distance calculations were performed using MEGA 6.06 software, and the phylogenetic trees were reconstructed using both MEGA 6.06 and IQ-Tree software. Finally, the secondary structure of ITS2 was modeled using the prediction tool in the ITS2 database. The results showed that ITS2 sequences of K. scoparia ranged in length from 226 to 227 bp, with a mean GC content of 55.3%. The maximum intraspecific distance was zero, while the minimum interspecific distance from closely related species and adulterants was 0.009 and 0.242, respectively. Kochia scoparia formed an independent clade in the phylogenetic trees, and its secondary structure exhibited enough variation to be separated from that of other species. In summary, ITS2 can be used as a mini-barcode for distinguishing K. scoparia from closely related species and adulterants. Its phylogenetic trees could illustrate the evolutionary process of K. scoparia in the Camphorosmeae. The phylogenetic results using ITS2 barcode further supported the internationally recognized revised classifications of Kochia and Bassia genera as a combined Bassia genus, together with the establishment of new genera Grubovia and Sedobassia, which we suggest is accepted by the Flora of China. Graphical abstract .
Collapse
|
39
|
Nishimaki T, Sato K. P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps. BMC Bioinformatics 2021; 22:36. [PMID: 33516169 PMCID: PMC7847139 DOI: 10.1186/s12859-021-03978-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022] Open
Abstract
Background Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates. Results We introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies. Conclusions P*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP.
Collapse
Affiliation(s)
- Takuma Nishimaki
- Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan
| | - Keiko Sato
- Department of Information Sciences, Tokyo University of Science, Noda City, Chiba, 278-8510, Japan.
| |
Collapse
|
40
|
Belintani T, Oliveira J, Pinotti H, Silva LA, Alevi KCC, Galvão C, Rosa JAD. Phylogenetic and phenotypic relationships of the Triatoma sordida subcomplex (Hemiptera: Reduviidae: Triatominae). Acta Trop 2020; 212:105679. [PMID: 32860747 DOI: 10.1016/j.actatropica.2020.105679] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 11/29/2022]
Abstract
Chagas disease, whose etiological agent is the protozoan Trypanosoma cruzi, affects millions of people worldwide and it is mainly transmitted by infected triatomine feces. Triatoma is the most diverse genus and one of the most important from an epidemiological point of view. Species of this genus are grouped into eight complexes and nine subcomplexes. Triatoma sordida subcomplex consists of T. garciabesi, T. guasayana, T. patagonica, and, T. sordida. Given the recent discussions on their phylogenetic status, this study aims to evaluate morphometric and genetics characters that group and distinguish T. garciabesi, T. guasayana, T. patagonica, and T. sordida, as well as to infer the phylogenetic relationships within the group and evaluate the proximity with T. rubrovaria subcomplex. The results corroborate the phylogenetic relationship of T. guasayana and T. patagonica with the T. rubrovaria subcomplex. Molecular data confirm the proximity of T. jurbergi, T. matogrossensis, T. vandae as T. garciabesi, and T. sordida. Together, genetic variability was shown between T. sordida populations.
Collapse
Affiliation(s)
- Tiago Belintani
- Institute of Biology, Campinas State University (Unicamp), Block O, Bertrand Russel Avenue, Campinas, São Paulo 13083-865, Brazil..
| | - Jader Oliveira
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara-Jaú Highway, km 1, Campos Ville, Araraquara, São Paulo 14800-903, Brazil
| | - Heloisa Pinotti
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara-Jaú Highway, km 1, Campos Ville, Araraquara, São Paulo 14800-903, Brazil
| | - Lucas Abrantes Silva
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara-Jaú Highway, km 1, Campos Ville, Araraquara, São Paulo 14800-903, Brazil
| | - Kaio Cesar Chaboli Alevi
- São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara-Jaú Highway, km 1, Campos Ville, Araraquara, São Paulo 14800-903, Brazil
| | - Cleber Galvão
- Laboratório Nacional e Internacional de Referência em Taxonomia de Triatomíneos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - João Aristeu da Rosa
- Institute of Biology, Campinas State University (Unicamp), Block O, Bertrand Russel Avenue, Campinas, São Paulo 13083-865, Brazil.; São Paulo State University (Unesp), School of Pharmaceutical Sciences, Araraquara-Jaú Highway, km 1, Campos Ville, Araraquara, São Paulo 14800-903, Brazil
| |
Collapse
|
41
|
Phukhamsakda C, McKenzie EHC, Phillips AJL, Gareth Jones EB, Jayarama Bhat D, Stadler M, Bhunjun CS, Wanasinghe DN, Thongbai B, Camporesi E, Ertz D, Jayawardena RS, Perera RH, Ekanayake AH, Tibpromma S, Doilom M, Xu J, Hyde KD. Microfungi associated with Clematis (Ranunculaceae) with an integrated approach to delimiting species boundaries. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00448-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
42
|
Lu Y, Li H, Li W, Wang X, Tao X, Dou L, Dong Y, Wu N, Li YG. Characterization of a G9 group A rotavirus reassortant strain detected in Jinzhou, China, in 2018-2019. Arch Virol 2020; 165:977-983. [PMID: 32095877 DOI: 10.1007/s00705-020-04563-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/25/2020] [Indexed: 02/06/2023]
Abstract
A novel rotavirus A (RVA) strain (JZ) was detected in RVA-positive stool specimens from three pediatric patients in Jinzhou, Liaoning Province, in 2018-2019. The electrophoresis pattern of the JZ strain showed a long electropherotype. The genomic constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 was detected, suggesting that a new inter-genogroup reassortment had occurred. Whole-genome sequencing showed that the JZ isolates were identical to each other. Phylogenetic analysis revealed that VP7 and VP4 clustered in lineages G9-VI and P[8]-3, respectively. JZ strain-specific amino acid substitutions were detected in VP7, VP4 and NSP4. This study provides information on the epidemiology and characteristics of G9 strains circulating in China.
Collapse
Affiliation(s)
- Ying Lu
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Hui Li
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Weiwei Li
- Women and Children's Hospital of Jinzhou, Jinzhou, China
| | - Xiaofang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Xiaoli Tao
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Lili Dou
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Ying Dong
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Nan Wu
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China
| | - Yong Gang Li
- Department of Pathogen Biology, College of Basic Medical Sciences, Jinzhou Medical University, Jinzhou, China.
| |
Collapse
|