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Huq MA, Rahman MS, Rahman MM. Aquincola agrisoli sp. nov., isolated from rhizospheric soil of eggplant and in silico genome mining for the prediction of biosynthetic gene clusters. Int J Syst Evol Microbiol 2024; 74. [PMID: 38683662 DOI: 10.1099/ijsem.0.006355] [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: 05/01/2024] Open
Abstract
A Gram-stain negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-54T, was isolated from the rhizospheric soil of eggplant. The colonies were observed to be light pink coloured, smooth, spherical and 0.2-0.6 mm in diameter when grown on R2A agar medium for 2 days. MAHUQ-54T was able to grow at 15-40 °C, at pH 5.5-9.0 and in the presence of 0-0.5 % NaCl (w/v). The strain gave positive results for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine, urea, Tween 20 and Tween 80. On the basis of the results of 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Aquincola and is closely related to Aquincola tertiaricarbonis L10T (98.8 % sequence similarity) and Leptothrix mobilis Feox-1T (98.2 %). MAHUQ-54T has a draft genome size of 5 994 516 bp (60 contigs), annotated with 5348 protein-coding genes, 45 tRNA and 5 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between MAHUQ-54T and its closest phylogenetic neighbours were 75.8-83.3 and 20.8-25.3 %, respectively. In silico genome mining revealed that MAHUQ-54T has a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 70.4 %. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). On the basis of dDDH, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAHUQ-54T represents a novel species within the genus Aquincola, for which the name Aquincola agrisoli sp. nov. is proposed, with MAHUQ-54T (=KACC 22001T = CGMCC 1.18515T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
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Chen C, Bai D, Zhang Z, Ding X, Yang S, Zhao Q, Zhang H. Describe the morphology and mitochondrial genome of Mecidea indica Dallas, 1851 (Hemiptera, Pentatomidae), with its phylogenetic position. PLoS One 2024; 19:e0299298. [PMID: 38547075 PMCID: PMC10977800 DOI: 10.1371/journal.pone.0299298] [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: 10/31/2023] [Accepted: 02/07/2024] [Indexed: 04/02/2024] Open
Abstract
We here describe the external morphology and complete mitochondrial genome characteristics of Mecidea indica Dallas, 1851, and clarify the evolutionary rate and divergence time. The M. indica mitochondrial genome length is 15,670 bp, and it exhibits a typical high A+T-skew (76.31%). The sequence shows strong synteny with the original gene arrangement of Drosophila yakuba Burla, 1954 without rearrangement. The M. indica mitochondrial genome characteristics were analyzed, and phylogenetic trees of Pentatomidae were reconstructed using Bayesian methods based on different datasets of the mitochondrial genome datasets. Phylogenetic analysis shows that M. indica belongs to Pentaotominae and form a sister-group with Anaxilaus musgravei Gross, 1976, and Asopinae is highly supported as monophyletic. Molecular clock analysis estimates a divergence time of Pentatomidae of 122.75 Mya (95% HPD: 98.76-145.43 Mya), within the Mesozoic Cretaceous; the divergence time of M. indica and A. musgravii was no later than 50.50 Mya (95% HPD: 37.20-64.80 Mya). In addition, the divergence time of Asopinae was 62.32 Mya (95% HPD: 47.08-78.23 Mya), which was in the Paleogene of the Cenozoic era. This study is of great significance for reconstructing the phylogeny of Pentatomidae and providing insights into its evolutionary history.
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Affiliation(s)
- Chao Chen
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Dongmei Bai
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Zhenhua Zhang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Xiaofei Ding
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shuzhen Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Hufang Zhang
- Department of Biology, Xinzhou Teachers University, Xinzhou, Shanxi, China
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [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: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Tang W, Li X, Ye B, Shi B, Zhang H, Dang Z, Sun Y, Danqu L, Xia C, Quzhen D, Zhao X, Chui W, Huang F. Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae). Ticks Tick Borne Dis 2024; 15:102311. [PMID: 38262211 DOI: 10.1016/j.ttbdis.2024.102311] [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: 05/06/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/25/2024]
Abstract
Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.
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Affiliation(s)
- Wenqiang Tang
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xin Li
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bijin Ye
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Bin Shi
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Haoji Zhang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Zhisheng Dang
- National Institute of Parasitic Diseases at China CDC/Chinese Center for Tropical Diseases Research, WHO Collaborating Centre for Tropical Diseases, NHC Key Laboratory for Parasite and Vector Biology, Shanghai 200025, China
| | - Yuexiang Sun
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China
| | - Lamu Danqu
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Chenyang Xia
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Danzeng Quzhen
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China; State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Tibet Lhasa 850002, China
| | - Xialing Zhao
- Institute of Animal Science, Tibet Academy of Agriculture and Animal Husbandry Sciences, Tibet Lhasa 850009, China
| | - Wenting Chui
- Animal Disease Prevention and Control Center of Qinghai Province, China
| | - Fuqiang Huang
- School of Life Science and Engineering, Foshan University, Guangdong Foshan 528225, China.
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Chhetri G, Kim MJ, Kim I, Tran DVH, Kim YW, Kim HW, Seo T. Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula. Front Microbiol 2024; 15:1361583. [PMID: 38495511 PMCID: PMC10940327 DOI: 10.3389/fmicb.2024.1361583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/08/2024] [Indexed: 03/19/2024] Open
Abstract
A novel halotolerant actinobacterium, designated as RG38T, capable of producing black extracellular melanin pigment on SP2 agar, was isolated from the roots of Tagetes patula. Comparative analysis of the 16S rRNA gene sequence revealed the highest similarity to Streptomyces collinus NBRC 12759T (99.3%). Phylogenetic analysis showed that strain RG38T clustered within the genus Streptomyces forming a monophyletic cluster with its close relatives. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and amino-acid identity (AAI) values between strain RG38T and related species within the genus Streptomyces were below the standard threshold for prokaryotic species delineation. The DNA G + C content of the strain RG38T was determined to be 73.3%. The genome size measured 7,150,598 bp comprising 17 contigs and encompassed 6,053 protein coding genes. AntiSMASH analysis of the whole genome revealed 35 putative biosynthetic gene clusters (BGCs) responsible for various secondary metabolites. Among these clusters, two gene clusters exhibited 100% similarity to the chromomycin A3, albaflavenone, and anthracimycin, respectively. These compounds were reported to possess significant anticancer and antibacterial activities. LC-MS-based analysis, coupled with further isolation studies, confirmed the production of chromomycins A2 (1), A3 (2), and their derivatives, along with their antibiotic activities. These findings underscore the potential of this novel strain as a novel resource for the discovery of diverse antimicrobial compounds. This study is the first to report an antimicrobial compound producing Streptomyces species isolated from medicinal plant T. patula. Based on a polyphasic study, the strain RG38T isolated from an unexplored habitat with a high potential for new natural products represents a novel species within the genus Streptomyces. Accordingly, we propose the name Streptomyces tagetis sp. nov. for this novel species, with the type strain is RG38T (=KCTC 49624T = TBRC 15113T).
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Affiliation(s)
- Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Myeong Ji Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Duc V. H. Tran
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Hyun Woo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang, Republic of Korea
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Matta T, Bhatia R, Joshi SR, Bishnoi M, Chopra K, Kondepudi KK. GABA synthesizing lactic acid bacteria and genomic analysis of Levilactobacillus brevis LAB6. 3 Biotech 2024; 14:62. [PMID: 38344283 PMCID: PMC10850046 DOI: 10.1007/s13205-024-03918-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 01/03/2024] [Indexed: 03/10/2024] Open
Abstract
This study was conducted to investigate the γ-aminobutyric acid (GABA) production ability of 20 Lactobacillus and 25 Bifidobacterium strains which were previously isolated in our laboratory. Effect of initial pH, incubation time, monosodium glutamate (MSG), and pyridoxal-5'-phosphate (PLP) concentration for highest GABA production by two potent bacterial strains, Levilactobacillus brevis LAB6 and Limosilactobacillus fermentum LAB19 were optimized in the MRS media. A threefold increase in GABA production at an initial pH 4.0, incubation time of 120 h in medium supplemented with 3% MSG and 400 μM of PLP for LAB6 and 300 μM for LAB19 lead to the production of 19.67 ± 0.28 and 20.77 ± 0.14 g/L of GABA, respectively. Coculturing both strains under optimized conditions led to a GABA yield of 20.02 ± 0.17 g/L. Owing to potent anti-inflammatory activity in-vitro, as reported previously, and highest GABA production ability of LAB6 (MTCC 25662), its whole-genome sequencing and bioinformatics analysis was carried out for mining genes related to GABA metabolism. LAB6 harbored a complete glutamate decarboxylase (GAD) gene system comprising gadA, gadB, and gadC as well as genes responsible for the beneficial probiotic traits, such as for acid and bile tolerance and host adhesion. Comparative genomic analysis of LAB6 with 28 completely sequenced Levilactobacillus brevis strains revealed the presence of 95 strain-specific genes-families that was significantly higher than most other L. brevis strains. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03918-7.
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Affiliation(s)
- Tushar Matta
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Pharmacology Research Laboratory, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014 India
| | - Ruchika Bhatia
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Santa Ram Joshi
- Department of Biotechnology & Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya 793022 India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
- Regional Centre of Biotechnology, Faridabad, India
| | - Kanwaljit Chopra
- Pharmacology Research Laboratory, University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014 India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Centre of Excellence in Functional Foods, Food and Nutrition Biotechnology Laboratory, National Agri-Food Biotechnology Institute, S. A. S. Nagar, Mohali, Punjab, 140306 India
- Department of Biotechnology, Panjab University, Chandigarh, India
- Regional Centre of Biotechnology, Faridabad, India
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Wang Z, Zhang W, Wang Z, Zhang Z, Liu Y, Liu S, Wu Q, Saiding E, Han J, Zhou J, Xu J, Yi X, Zhang Z, Wang R, Su X. Analysis of antimicrobial biological activity of a marine Bacillus velezensis NDB. Arch Microbiol 2024; 206:131. [PMID: 38421449 DOI: 10.1007/s00203-024-03861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
A new strain of Bacillus velezensis NDB was isolated from Xiangshan Harbor and antibacterial test revealed antibacterial activity of this strain against 12 major pathogenic bacteria. The whole genome of the bacterium was sequenced and found to consist of a 4,214,838 bp circular chromosome and a 7410 bp circular plasmid. Furthermore, it was predicted by AntiSMASH and BAGEL4 to have 12 clusters of secondary metabolism genes for the synthesis of the inhibitors, fengycin, bacillomycin, macrolactin H, bacillaene, and difficidin, and there were also five clusters encoding potentially novel antimicrobial substances, as well as three bacteriocin biosynthesis gene clusters of amylocyclicin, ComX1, and LCI. qRT-PCR revealed significant up-regulation of antimicrobial secondary metabolite synthesis genes after 24 h of antagonism with pathogenic bacteria. Furthermore, MALDI-TOF mass spectrometry revealed that it can secrete surfactin non-ribosomal peptide synthase and polyketide synthase to exert antibacterial effects. GC-MS was used to analyze methanol extract of B. velezensis NDB, a total of 68 compounds were identified and these metabolites include 16 amino acids, 17 acids, 3 amines, 11 sugars, 11 alcohols, 1 ester, and 9 other compounds which can inhibit pathogenic bacteria by initiating the antibiotic secretion pathway. A comparative genomic analysis of gene families showed that the specificity of B. velezensis NDB was mainly reflected in environmental adaptability. Overall, this research on B. velezensis NDB provides the basis for elucidating its biocontrol effect and promotes its future application as a probiotic.
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Affiliation(s)
- Ze Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Wenwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Zhixuan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Yan Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Songyi Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Qiaoli Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Emilaguli Saiding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Jiajie Xu
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China
| | - Xianghua Yi
- Xiangshan Lanshang Marine Technology Co., Ltd, Ningbo, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China.
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China.
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China.
| | - Rixin Wang
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China.
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China.
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, 169 Qixing South Road, Ningbo, China.
- Key Laboratory of Aquacultural Biotechnology Ministry of Education, Ningbo University, 169 Qixing South Road, Ningbo, China.
- School of Marine Science, Ningbo University, 169 Qixing South Road, Ningbo, China.
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Das R, Nadar K, Arora R, Bajpai U. Unlocking prophage potential: In silico and experimental analysis of a novel Mycobacterium fortuitum LysinB containing a peptidoglycan-binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580446. [PMID: 38405724 PMCID: PMC10888907 DOI: 10.1101/2024.02.15.580446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Endolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as highly specific lytic proteins with a low chance of bacterial resistance. The diversity in lysin sequences and domain organization can be staggering. In silico analysis of bacteriophage and prophage genomes can help identify endolysins exhibiting unique features and high antibacterial activity, hence feeding the pipeline of narrow-spectrum protein antibiotics. Mycobacteriophage lysis cassettes mostly have two lytic enzymes, LysinA and LysinB. The enzyme LysinA targets peptidoglycan in the cell wall and possesses a modular architecture. LysinB typically contains a single domain and acts upon the mycolyl ester linkages in mycolyl-arabinogalactan-peptidoglycan (Payne et al., 2010). This study aimed to find novel LysinBs against Mycobacterium fortuitum. After a detailed in silico characterization of lysis cassettes from three M. fortuitum prophages, we chose to work on a LysinB (hereafter described as LysinB_MF) found in an incomplete prophage (phiE1336, 9.4 kb in strain E1336). LysinB_MF showed low sequence similarity with any other endolysins in the database and formed a separate clade on phylogenetic analysis. LysinB_MF's structure, extracted from the AlphaFold Protein Structure Database, demonstrated a modular architecture with two structurally distinct domains: a peptidoglycan-binding domain (PGBD) at the N-terminal and the characteristic alpha/beta hydrolase domain connected via a linker peptide. We found the alpha/beta hydrolase domain, which is the enzyme-active domain (EAD), contains the conserved Ser-Asp-His catalytic triad with a tunnel-like topology and forms intermolecular hydrogen bonds. The PGBD shows structural similarity to the cell-wall binding domain of an amidase from Clostridium acetobutylicum, hinting at its acquisition due to domain mobility. Our in silico electrostatic potential analysis suggested that PGBD might be essential to the enzyme activity. This was experimentally validated by generating a truncated version of the enzyme, which demonstrated about six-fold decreased activity compared to its native form. The antimycobacterial activity of this enzyme was also compromised in its absence. Based on our analysis, PGBD emerged as an integral constituent of enzymes with diverse functional properties and is predicted to be a conserved cross-kingdom. Overall, this study highlights the importance of mining mycobacterial prophages as a novel endolysin source. It also provides unique insights into the diverse architecture of mycobacteriophage-encoded endolysins and the importance of functional domains for their catalytic activities.
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Affiliation(s)
- Ritam Das
- Faculty of Biological Sciences, Friedrich Schiller University, Jena-07737, Germany
- Department of Life Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Kanika Nadar
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Ritu Arora
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
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An M, Liang R, Lu Y, Li X, Zhao G. Thiopseudomonas acetoxidans sp. nov., an aerobic acetic and butyric acids oxidizer isolated from anaerobic fermentation liquid of food waste. Antonie Van Leeuwenhoek 2024; 117:35. [PMID: 38351143 DOI: 10.1007/s10482-024-01932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
A Gram-stain-negative, oxidase-negative, rod-shaped, motile, facultatively anaerobic bacterial strain, designated as CY1220T, was isolated from an anaerobic fermentation liquid of food waste treatment plant. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain CY1220T belongs to the genus Thiopseudomonas, with the highest sequence similarity to Thiopseudomonas alkaliphila B4199T (95.91%), followed by Thiopseudomonas denitrificans X2T (95.56%). The genomic DNA G + C content of strain CY1220T was 48.6 mol%. The average nucleotide identity values and digital DNA-DNA hybridization values between strain CY1220T and the type species of T. alkaliphila and T. denitrificans were in the range of 70.8-71.6% and 19.2-20.0%, respectively, below the thresholds for species delineation. The strain was able to grow utilizing acetic acid and butyric acid (AABA) as the sole carbon source in aerobic conditions. Genomic analysis predicted that the strain could synthesize vitamin B12 and ectoine. The predominant cellular fatty acids were C18:1 ω7c and/or C18:1 ω6c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C12:0. The polar lipids comprised diphosphatidylglycerol, unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Q-8 (2.1%) and Q-9 (97.9%) were detected as the respiratory quinones. Based on its phenotypic, genotypic and genomic characteristics, strain CY1220T represents a novel species in the genus Thiopseudomonas, for which the name Thiopseudomonas acetoxidans sp. nov. is proposed. The type strain is CY1220T (= GDMCC 1.3503 T = JCM 35747 T).
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Affiliation(s)
- Miaomiao An
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ruina Liang
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanjuan Lu
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing, 100085, China
| | - Xiaoxu Li
- Beijing Fairyland Environmental Technology Co., Ltd, Beijing, 100085, China
| | - Guozhu Zhao
- Beijing Key Laboratory of Food Processing and Safety in Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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Xu Y, Liang X, Hyun CG. Isolation, Characterization, Genome Annotation, and Evaluation of Tyrosinase Inhibitory Activity in Secondary Metabolites of Paenibacillus sp. JNUCC32: A Comprehensive Analysis through Molecular Docking and Molecular Dynamics Simulation. Int J Mol Sci 2024; 25:2213. [PMID: 38396889 PMCID: PMC10889091 DOI: 10.3390/ijms25042213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
A potential strain, Paenibacillus sp. JNUCC32, was isolated and subjected to whole-genome sequencing. Genome functional annotation revealed its active metabolic capabilities. This study aimed to investigate the pivotal secondary metabolites in the biological system. Fermentation and extraction were performed, resulting in the isolation of seven known compounds: tryptophol (1), 3-(4-hydroxyphenyl)propionic acid (2), ferulic acid (3), maculosin (4), brevianamide F (5), indole-3-acetic acid (6), and butyric acid (7). Tryptophol exhibited favorable pharmacokinetic properties and demonstrated certain tyrosinase inhibitory activity (IC50 = 999 μM). For further analysis of its inhibition mechanism through molecular docking and molecular dynamics (MD) simulation, tryptophol formed three hydrogen bonds and a pro-Michaelis complex with tyrosinase (binding energy = -5.3 kcal/mol). The MD simulation indicated favorable stability for the tryptophol-mushroom tyrosinase complex, primarily governed by hydrogen bond interactions. The crucial residues VAL-283 and HIS-263 in the docking were also validated. This study suggests tryptophol as a potential candidate for antibrowning agents and dermatological research.
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Affiliation(s)
| | | | - Chang-Gu Hyun
- Department of Beauty and Cosmetology, Jeju Inside Agency and Cosmetic Science Center, Jeju National University, Jeju 63243, Republic of Korea; (Y.X.); (X.L.)
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Evseev PV, Shneider MM, Kolupaeva LV, Kasimova AA, Timoshina OY, Perepelov AV, Shpirt AM, Shelenkov AA, Mikhailova YV, Suzina NE, Knirel YA, Miroshnikov KA, Popova AV. New Obolenskvirus Phages Brutus and Scipio: Biology, Evolution, and Phage-Host Interaction. Int J Mol Sci 2024; 25:2074. [PMID: 38396752 PMCID: PMC10888812 DOI: 10.3390/ijms25042074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Two novel virulent phages of the genus Obolenskvirus infecting Acinetobacter baumannii, a significant nosocomial pathogen, have been isolated and studied. Phages Brutus and Scipio were able to infect A. baumannii strains belonging to the K116 and K82 capsular types, respectively. The biological properties and genomic organization of the phages were characterized. Comparative genomic, phylogenetic, and pangenomic analyses were performed to investigate the relationship of Brutus and Scipio to other bacterial viruses and to trace the possible origin and evolutionary history of these phages and other representatives of the genus Obolenskvirus. The investigation of enzymatic activity of the tailspike depolymerase encoded in the genome of phage Scipio, the first reported virus infecting A. baumannii of the K82 capsular type, was performed. The study of new representatives of the genus Obolenskvirus and mechanisms of action of depolymerases encoded in their genomes expands knowledge about the diversity of viruses within this taxonomic group and strategies of Obolenskvirus-host bacteria interaction.
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Affiliation(s)
- Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Lyubov V. Kolupaeva
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
| | - Anastasia A. Kasimova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Olga Y. Timoshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Andrey V. Perepelov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Anna M. Shpirt
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Andrey A. Shelenkov
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia (Y.V.M.)
| | - Yulia V. Mikhailova
- Central Scientific Research Institute of Epidemiology, 111123 Moscow, Russia (Y.V.M.)
| | - Natalia E. Suzina
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Center for Biological Research of the Russian Academy of Sciences”, Moscow Region, 142290 Pushchino, Russia;
| | - Yuriy A. Knirel
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia; (A.V.P.); (A.M.S.); (Y.A.K.)
| | - Konstantin A. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.S.); (O.Y.T.); (K.A.M.)
| | - Anastasia V. Popova
- State Research Center for Applied Microbiology and Biotechnology, City District Serpukhov, Moscow Region, 142279 Obolensk, Russia; (L.V.K.); (A.A.K.)
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Amin A, Noureen R, Iftikhar A, Hussain A, Alonazi WB, Raza HMZ, Ferheen I, Ibrahim M. Uropathogenic bacteria and deductive genomics towards antimicrobial resistance, virulence, and potential drug targets. Int Microbiol 2024; 27:325-335. [PMID: 37553507 DOI: 10.1007/s10123-023-00416-3] [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: 04/22/2023] [Revised: 07/15/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023]
Abstract
Urinary tract infections (UTIs) are among the most prevalent bacterial infections affecting people in inpatient and outpatient settings. The current study aimed to sequence the genome of uropathogenic Escherichia coli strain CUI-B1 resourced from a woman having uncomplicated cystitis and pyelonephritis. Followed by deductive genomics towards potential drug targets using E. coli strain CUI-B1, strain O25b: H4-ST131, Proteus mirabilis strain HI4320, Klebsiella pneumoniae strain 1721, and Staphylococcus saprophyticus strain ATCC 15305 uropathogenic strains. Comparative genome analysis revealed that genes related to the survival of E. coli, P. mirabilis, K. pneumoniae, and S. saprophyticus, such as genes of metal-requiring proteins, defense-associated genes, and genes associated with general physiology, were found to be highly conserved in the genomes including strain CUI-B1. However, the genes responsible for virulence and drug resistance, mainly those that are involved in bacterial secretion, fimbriae, adherence, and colonization, were found in various genomic regions and varied from one species to another or within the same species. Based on the genome sequence, virulence, and antimicrobial-resistant gene dataset, the subtractive proteomics approach revealed 22 proteins mapped to the pathogen's unique pathways and among them, entB, clbH, chuV, and ybtS were supposed to be potential drug targets and the single drug could be utilized for all above-mentioned strains. These results may provide the foundation for the optimal target for future discovery of drugs for E. coli-, P. mirabilis-, K. pneumoniae-, and S. saprophyticus-based infections and could be investigated further to employ in personalized drug development.
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Affiliation(s)
- Aaima Amin
- Medical Department, Quaid e Azam Medical College, Bahawalpur, Pakistan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Ramisha Noureen
- Medical Department, Fatima Jinnah Medical University, Lahore, Pakistan
| | - Ayesha Iftikhar
- Medical Department, Govt Khawaja Muhammad Safdar Medical Collage, Sialkot, Pakistan
| | - Annam Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Wadi B Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh, 11587, Saudi Arabia
| | | | - Ifra Ferheen
- Laboratory of Genetics of Microorganisms, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan.
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Zhang J, Shu L, Peng Z. Adaptive evolution of mitochondrial genomes in Triplophysa cavefishes. Gene 2024; 893:147947. [PMID: 37923093 DOI: 10.1016/j.gene.2023.147947] [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: 07/05/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Extreme conditions in caves pose survival challenges for cave dwellers, who gradually develop adaptive survival features. Cavefishes are one of the most successful animals among cave dwellers. Triplophysa cavefishes are an important group of cavefishes, and they show remarkable adaptability to the extreme environments of caves. However, there is a limited understanding of their adaptation mechanisms. In this study, eight complete mitochondrial genomes of Triplophysa cavefishes were newly obtained, and their genomic characteristics, including the base composition, base bias, and codon usage, were analyzed. Phylogenetic analysis was carried out based on 13 mitochondrial protein-coding genes from 44 Nemacheilidae species. This showed that Triplophysa cavefishes and non-cavefishes separate into two reciprocally monophyletic clades, suggesting a single origin of the cave phenotype. Positive selection analysis strongly suggested that the selection pressure in cavefishes is higher than that in non-cavefishes. Furthermore, the ND5 gene in cavefishes showed evidence of positive selection, which suggests that the gene may play an important role in the adaptation of cavefishes to the cave environment. Protein structure analysis of the ND5 subunit implied that the sites of positive selection in cavefishes might allow them to acquire lower ND5 protein stability, compared to that in non-cavefishes, which might help the accumulation of nonsynonymous (mildly deleterious) mutations. Together, our study revealed the genetic signatures of cave adaptation in Triplophysa cavefishes from the perspective of energy metabolism.
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Affiliation(s)
- Jiatong Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | - Lu Shu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400715, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China.
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64
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Rhoads DD, Pummill J, Alrubaye AAK. Molecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers. Microorganisms 2024; 12:250. [PMID: 38399654 PMCID: PMC10892122 DOI: 10.3390/microorganisms12020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all the sepsis isolates. Core genome single nucleotide polymorphism analyses have identified a number of mutations, affecting the protein-coding sequences, that are enriched in sepsis isolates. The analysis of the protein substitutions supports the mutational origins of sepsis isolates.
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Affiliation(s)
- Douglas D. Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jeff Pummill
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adnan Ali Khalaf Alrubaye
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR 72701, USA; (J.P.); (A.A.K.A.)
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
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Tang Y, Ma W, Chen X, Nie G, Zhou C. Four new complete mitochondrial genomes of Gobioninae fishes (Teleostei: Cyprinidae) and their phylogenetic implications. PeerJ 2024; 12:e16632. [PMID: 38259668 PMCID: PMC10802160 DOI: 10.7717/peerj.16632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.
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Affiliation(s)
- Yongtao Tang
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Wenwen Ma
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Xin Chen
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Guoxing Nie
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
| | - Chuanjiang Zhou
- College of Fisheries, Engineering Technology Research Center of Henan Province for Aquatic Animal Cultivation, Henan Normal University, Xinxiang, Henan province, The People’s Republic of China
- College of Life Sciences, Henan Normal University, Xinxiang, Henan Province, China
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Li DM, Pan YG, Liu HL, Yu B, Huang D, Zhu GF. Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships. BMC Genomics 2024; 25:68. [PMID: 38233753 PMCID: PMC10792896 DOI: 10.1186/s12864-024-09996-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in the tropical regions of South America, Africa, and Southeast Asia, of which some species have important ornamental, medicinal and ecological values. Previous studies on the phylogenetic and taxonomic of Costaceae by using nuclear internal transcribed spacer (ITS) and chloroplast genome fragments data had low resolutions. Additionally, the structures, variations and molecular evolution of complete chloroplast genomes in Costaceae still remain unclear. Herein, a total of 13 complete chloroplast genomes of Costaceae including 8 newly sequenced and 5 from the NCBI GenBank database, representing all three distribution regions of this family, were comprehensively analyzed for comparative genomics and phylogenetic relationships. RESULT The 13 complete chloroplast genomes of Costaceae possessed typical quadripartite structures with lengths from 166,360 to 168,966 bp, comprising a large single copy (LSC, 90,802 - 92,189 bp), a small single copy (SSC, 18,363 - 20,124 bp) and a pair of inverted repeats (IRs, 27,982 - 29,203 bp). These genomes coded 111 - 113 different genes, including 79 protein-coding genes, 4 rRNA genes and 28 - 30 tRNAs genes. The gene orders, gene contents, amino acid frequencies and codon usage within Costaceae were highly conservative, but several variations in intron loss, long repeats, simple sequence repeats (SSRs) and gene expansion on the IR/SC boundaries were also found among these 13 genomes. Comparative genomics within Costaceae identified five highly divergent regions including ndhF, ycf1-D2, ccsA-ndhD, rps15-ycf1-D2 and rpl16-exon2-rpl16-exon1. Five combined DNA regions (ycf1-D2 + ndhF, ccsA-ndhD + rps15-ycf1-D2, rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1, ccsA-ndhD + rpl16-exon2-rpl16-exon1, and ccsA-ndhD + rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1) could be used as potential markers for future phylogenetic analyses and species identification in Costaceae. Positive selection was found in eight protein-coding genes, including cemA, clpP, ndhA, ndhF, petB, psbD, rps12 and ycf1. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed identical tree topologies with high supports between species of Costaceae. Three clades were divided within Costaceae, including the Asian clade, Costus clade and South American clade. Tapeinochilos was a sister of Hellenia, and Parahellenia was a sister to the cluster of Tapeinochilos + Hellenia with strong support in the Asian clade. The results of molecular dating showed that the crown age of Costaceae was about 30.5 Mya (95% HPD: 14.9 - 49.3 Mya), and then started to diverge into the Costus clade and Asian clade around 23.8 Mya (95% HPD: 10.1 - 41.5 Mya). The Asian clade diverged into Hellenia and Parahellenia at approximately 10.7 Mya (95% HPD: 3.5 - 25.1 Mya). CONCLUSION The complete chloroplast genomes can resolve the phylogenetic relationships of Costaceae and provide new insights into genome structures, variations and evolution. The identified DNA divergent regions would be useful for species identification and phylogenetic inference in Costaceae.
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Affiliation(s)
- Dong-Mei Li
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Yan-Gu Pan
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hai-Lin Liu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bo Yu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dan Huang
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Gen-Fa Zhu
- Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Gao RR, Lei QL, Jin X, Zafar I, Yang XK, Su CY, Hao JS, Nie RE. Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications. INSECTS 2024; 15:50. [PMID: 38249056 PMCID: PMC10816406 DOI: 10.3390/insects15010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.
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Affiliation(s)
- Rong-Rong Gao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Qi-Long Lei
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Xu Jin
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Iqbal Zafar
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Xing-Ke Yang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou 510260, China
| | - Cheng-Yong Su
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Jia-Sheng Hao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
| | - Rui-E Nie
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China; (R.-R.G.); (X.J.); (I.Z.); (C.-Y.S.)
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Skalon EK, Starunova ZI, Petrov SA, Smirnov RV, Zaitseva OV, Starunov VV. The Mitochondrial Genomes of Siboglinum plumosum and Oligobrachia dogieli (Annelida: Siboglinidae) and Their Phylogenetic Analysis. Genes (Basel) 2024; 15:77. [PMID: 38254966 PMCID: PMC10815697 DOI: 10.3390/genes15010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/25/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Frenulates are a group of sedentary Annelida within the family Siboglinidae that inhabit the ocean floor and present a unique challenge for comprehensive molecular and phylogenetic investigations. In this study, we focused on the frenulates, specifically assembling the mitochondrial genomes of Siboglinum plumosum and Oligobrachia dogieli. The phylogenetic reconstruction placed S. plumosum as a sister taxon to S. ekmani, and O. dogieli as a sister taxon to S. fiordicum, supporting the non-monophyletic nature of the genus Siboglinum. Overall, this study supports the phylogeny of the family Siboglinidae while highlighting the need for additional molecular data within frenulates.
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Affiliation(s)
| | | | | | | | | | - Viktor V. Starunov
- Zoological Institute, Russian Academy of Sciences, 199034 Saint-Petersburg, Russia; (E.K.S.); (Z.I.S.); (S.A.P.); (R.V.S.); (O.V.Z.)
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Sharma M, Singh DN, Uttam G, Sharma P, Meena SA, Verma AK, Negi RK. Adaptive evolution of Sphingopyxis sp. MC4 conferred degradation potential for persistent β- and δ-Hexachlorocyclohexane (HCH) isomers. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132545. [PMID: 37757562 DOI: 10.1016/j.jhazmat.2023.132545] [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: 02/20/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Hexachlorocyclohexane (HCH), an organochlorine pesticide imposes several harmful impacts on the ecosystem. β- and δ-isomers of HCH are highly toxic, persistent, and recalcitrant to biodegradation, slow and incomplete degradation of β- and δ- isomers have been reported in a few strains. We have isolated a strain designated as Sphingopyxis strain MC4 that can tolerate and degrade high concentrations of α-, β-, γ- and δ-HCH isomers. To date, no other Sphingopyxis strain has been reported to degrade β- and δ-isomers. To understand the underlying genetic makeup contributing to adaptations, the whole genome of strain MC4 was sequenced. Comparative genome analysis showed that strain MC4 harbors the complete pathway (lin genes) required for HCH degradation. Genetic footprints such as presence of lin genes on genomic islands, IS6100 elements in close proximity of lin genes, and synteny in lin flanking regions with other strains reflects the horizontal gene transfer in strain MC4. Positive selection and HGT drive the adaptive evolution of strain MC4 under the pressure of HCH contamination that it experienced in its surrounding niche. In silico analyses showed efficient binding of β- and δ-isomers with enzymes leading to rapid degradation that need further validation by cloning and biochemical experiments.
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Affiliation(s)
- Monika Sharma
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Durgesh Narain Singh
- Department of Zoology, University of Delhi, Delhi 110007, India; BioNEST-BHU, InnoResTech Foundation, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Gunjan Uttam
- Zoology section, MMV, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Poonam Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Shivam A Meena
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Akhilesh K Verma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Ram Krishan Negi
- Department of Zoology, University of Delhi, Delhi 110007, India.
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Elameen A, Maduna SN, Mageroy MH, van Eerde A, Knudsen G, Hagen SB, Eiken HG. Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae. BMC Genomics 2024; 25:21. [PMID: 38166583 PMCID: PMC10759517 DOI: 10.1186/s12864-023-09905-1] [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: 06/23/2023] [Accepted: 12/14/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops. RESULTS The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae. CONCLUSIONS Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.
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Affiliation(s)
- Abdelhameed Elameen
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway.
| | - Simo N Maduna
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Melissa H Mageroy
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - André van Eerde
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Geir Knudsen
- Division of Biotechnology and Plant Health, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Snorre B Hagen
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
| | - Hans Geir Eiken
- Division of Environment and Natural Resources, NIBIO, Norwegian Institute of Bioeconomy Research, Høghskoleveien 7, N-1431, Aas, Norway
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Díaz-García L, Chuvochina M, Feuerriegel G, Bunk B, Spröer C, Streit WR, Rodriguez-R LM, Overmann J, Jiménez DJ. Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes. Syst Appl Microbiol 2024; 47:126485. [PMID: 38211536 DOI: 10.1016/j.syapm.2023.126485] [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: 07/18/2023] [Revised: 10/19/2023] [Accepted: 12/01/2023] [Indexed: 01/13/2024]
Abstract
An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.
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Affiliation(s)
- Laura Díaz-García
- Department of Chemical and Biological Engineering, Advanced Biomanufacturing Centre, University of Sheffield, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia
| | - Golo Feuerriegel
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; Braunschweig University of Technology, Braunschweig, Germany
| | - Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia; Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.
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Li C, Gao Y, Wang D, Dang L. The extraordinary rearrangement of mitochondrial genome of the wheat pest, Aptinothrips stylifer and the mitochondrial phylogeny of Thripidae (Thysanoptera). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22086. [PMID: 38288496 DOI: 10.1002/arch.22086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
The mitochondrial gene order in Thysanoptera is notably distinct and highly rearranged, with each species exhibiting its own unique arrangement. To elucidate the relationship between gene rearrangements and phylogeny, the complete mitochondrial genome (mitogenome) of the wheat pest, Aptinothrips stylifer, was sequenced and assembled, spanning a total length of 16,033 bp. Compared with the ancestral arthropod mitogenome, significant rearrangement differences were evident in A. stylifer, whereas the gene order between A. stylifer and Anaphothrips obscurus was similar. Phylogenetic trees were reconstructed based on all 13 protein-coding gene sequences using Bayesian inference and maximum-likelihood methods, both yielding similar topological structures. Notably, A. stylifer was robustly clustered with A. obscurus, affirming its classification within Anaphothrips genus group. This exemplifies the potential correlation between gene rearrangements and phylogeny in the Thripidae family. Additionally, the mitogenome of A. stylifer exhibited several atypical features, including: (1) Three putative control regions (CRs) in close proximity, with CR2 and CR3 displaying partial similarity, and CR1 differing in base composition; (2) Two transfer RNAs (tRNAs), trnS1 and trnV, lacking the DHU arm; (3) Two ribosomal RNA (rRNA) genes inverted and positioned distant from each other; (4) Negative AT and GC skew (AT skew = -0.001, GC skew = -0.077); (5) One transposition (nad6), one inverse transposition (trnQ), four inversions (trnF, trnH, trnC, and gene block nad1-trnL1-rrnL-trnV-rrnS), and four tandem duplication random loss events; and (6) Two protein-coding genes, nad2 and atp8, terminated with an incomplete stop codon "T".
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Affiliation(s)
- Chengwen Li
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Yuxin Gao
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Dongxue Wang
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Lihong Dang
- Department of Biology, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong, China
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Long M, Chen D, Fan H, Tang S, Gan Z, Xia H, Lu Y. Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer. Int J Syst Evol Microbiol 2024; 74. [PMID: 38240737 DOI: 10.1099/ijsem.0.006209] [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: 01/23/2024] Open
Abstract
A Gram-negative, non-motile, strictly aerobic, rod-shaped bacterium, designated as H12T, was isolated from the sediments of mangrove plant Bruguiera sexangula taken from Dapeng district, Shenzhen, PR China. The pairwise 16S rRNA gene sequence analysis showed that strain H12T shared high identity levels with species of the genus Microbulbifer, with the highest similarity level of 98.5 % to M. pacificus SPO729T, followed by 98.1 % to M. donghaiensis CN85T. Phylogenetic analysis using core-genome sequences showed that strain H12T formed a cluster with type species of M. pacificus SPO729T and M. harenosus HB161719T. The complete genome of strain H12T was 4 481 396 bp in size and its DNA G+C content was 56.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values among strain H12T and type species of genus Microbulbifer were below the cut-off levels of 95-96 and 70 %, respectively. The predominant cellular fatty acids of strain H12T were iso-C15 : 0 (22.5 %) and C18 : 1 ω7c (13.9 %). Ubiquinone-8 was detected as the major respiratory quinone. The polar lipids of strain H12T comprised one phosphatidylglycerol, one phosphatidylethanolamine, one unidentified aminoglycophospholipid, one unidentified glycophospholipid, three unidentified glycolipids, two unidentified aminolipids, and one unidentified lipid. Based on polyphasic evidence, strain H12T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer bruguierae sp. nov. is proposed. The type strain is H12T (=KCTC 92859T=MCCC 1K08451T). Comparative genomic analyses of strain H12T with strains of the genus Microbulbifer reveal its potential in degradation of pectin.
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Affiliation(s)
- Meng Long
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Dakun Chen
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Huimin Fan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Shaoshuai Tang
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Zhen Gan
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
| | - Hongli Xia
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
| | - Yishan Lu
- Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, and Shenzhen Public Service Platform for Evaluation of Marine Economic Animal Seedings, Shenzhen Institute of Guangdong Ocean University, Shenzhen, PR China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, and Key Laboratory of Control for Disease of Aquatic Animals of Guangdong Higher Education Institute, College of Fishery, Guangdong Ocean University, Zhanjiang, PR China
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Li SY, Chen MH, Sun L, Wang RH, Li CH, Gresens S, Li Z, Lin XL. New mitogenomes from the genus Cricotopus (Diptera: Chironomidae, Orthocladiinae): Characterization and phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22067. [PMID: 38014568 DOI: 10.1002/arch.22067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Cricotopus is a large and diverse genus of non-biting midges composed of several subgenera. Complete mitogenome sequences are available for very few Cricotopus species. The subgenus Pseudocricotopus unites species with unusual morphological structures in adult male and pupal stages, however, molecular methods are needed to verify the placement of this subgenus within Cricotopus. We obtained mitogenomes of C. (Pseudocricotopus) cf. montanus and nine other Cricotopus species for phylogenetic analysis, coupled with two Rheocricotopus species and one Synorthocladius species as outgroups. The structure of the mitogenome was similar among these Cricotopus species, exhibiting A+T bias and retaining ancestral gene order. Mutation rate, estimated as Ka/Ks, varied among genes, and was highest for ATP8 and lowest for COI. The phylogenetic relationships among species of Cricotopus, Rheocricotopus and Synorthocladius was reconstructed using Bayesian inference and maximum likelihood estimation. The phylogenetic trees confirmed placement of subgenus Pseudocricotopus, represented by Cricotopus cf. montanus, within Cricotopus. Our study increases the library of chironomid mitogenomes and provides insight into the properties of their constituent genes.
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Affiliation(s)
- Shu-Yi Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Meng-Han Chen
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Li Sun
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Rui-Hao Wang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Chen-Hong Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Susan Gresens
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Zhao Li
- China National Environmental Monitoring Centre, Beijing, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
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75
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Xie J, Miao Y, Zhang X, Zhang G, Guo B, Luo G, Huang L. Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis. JOURNAL OF PLANT RESEARCH 2024; 137:37-48. [PMID: 37917204 DOI: 10.1007/s10265-023-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023]
Abstract
Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum. Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum, and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris. This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum.
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Affiliation(s)
- Junbo Xie
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China
| | - Yujing Miao
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Xinke Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guoshuai Zhang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China
| | - Guangming Luo
- School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China.
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China.
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Medina JE, Castañeda S, Páez-Triana L, Camargo M, Garcia-Corredor DJ, Gómez M, Luna N, Ramírez AL, Pulido-Medellín M, Muñoz M, Ramírez JD. High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 117:105543. [PMID: 38135265 DOI: 10.1016/j.meegid.2023.105543] [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: 11/13/2023] [Revised: 12/13/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.
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Affiliation(s)
- Julián Esteban Medina
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luisa Páez-Triana
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Funza, Cundinamarca, Colombia
| | - Diego J Garcia-Corredor
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marcela Gómez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Grupo de Investigación en Ciencias Básicas (NÚCLEO) Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie L Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Martín Pulido-Medellín
- Grupo de Investigación en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología - UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
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Cheng Y, Zhu W, Han S, Yang J, Wu G, Zhao G, He X. Roseomonas populi sp. nov., an acetate-degrading bacteria isolated from the stem of Populus tomentosa. Antonie Van Leeuwenhoek 2023; 117:2. [PMID: 38147266 DOI: 10.1007/s10482-023-01911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 12/27/2023]
Abstract
Strain CN29T, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29T were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29T was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75T (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29T and Roseomonas populi CN29T were 82.7% and 27.8%, respectively. The genome size of strain CN29T was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c and C16:0. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29T can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29T strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29T is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29T (= JCM 35579T = GDMCC 1.3267T).
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Affiliation(s)
- Yao Cheng
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wen Zhu
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuo Han
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Yang
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guanqi Wu
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Guozhu Zhao
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiangwei He
- Beijing Key Laboratory of Food Processing and Safety, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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78
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Li K, Yu SW, Hu H, Feng YF, Storey KB, Ma Y, Zhang JY, Yu DN. The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes. Genes (Basel) 2023; 15:13. [PMID: 38275595 PMCID: PMC10815127 DOI: 10.3390/genes15010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.
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Affiliation(s)
- Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Sheng-Wu Yu
- Longquan Protection Center of Qianjiangyuan-Baishanzu National Park, Lishui 323700, China
| | - Hao Hu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yu-Feng Feng
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Yue Ma
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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79
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Riva A, Rasoulimehrabani H, Cruz-Rubio JM, Schnorr SL, von Baeckmann C, Inan D, Nikolov G, Herbold CW, Hausmann B, Pjevac P, Schintlmeister A, Spittler A, Palatinszky M, Kadunic A, Hieger N, Del Favero G, von Bergen M, Jehmlich N, Watzka M, Lee KS, Wiesenbauer J, Khadem S, Viernstein H, Stocker R, Wagner M, Kaiser C, Richter A, Kleitz F, Berry D. Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting. Nat Commun 2023; 14:8210. [PMID: 38097563 PMCID: PMC10721620 DOI: 10.1038/s41467-023-43448-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023] Open
Abstract
Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.
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Affiliation(s)
- Alessandra Riva
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Chair of Nutrition and Immunology, School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Hamid Rasoulimehrabani
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - José Manuel Cruz-Rubio
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Stephanie L Schnorr
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Cornelia von Baeckmann
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Deniz Inan
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Georgi Nikolov
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Andreas Spittler
- Core Facility Flow Cytometry and Surgical Research Laboratories, Medical University of Vienna, Vienna, Austria
| | - Márton Palatinszky
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Aida Kadunic
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Norbert Hieger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Giorgia Del Favero
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz Centre for Environmental Research, Department of Molecular Systems Biology, Leipzig, Germany
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Kang Soo Lee
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Julia Wiesenbauer
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Sanaz Khadem
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Helmut Viernstein
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Vienna, Austria
| | - Freddy Kleitz
- Department of Functional Materials and Catalysis, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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Kobierecka P, Wyszyńska A, Aleksandrzak-Piekarczyk T, Sałańska A, Gawor J, Bardowski J, Jagusztyn Krynicka KE. Genomic and transcriptomic analysis of Ligilactobacillus salivarius IBB3154-in search of new promoters for vaccine construction. Microbiol Spectr 2023; 11:e0284423. [PMID: 37982628 PMCID: PMC10715006 DOI: 10.1128/spectrum.02844-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE The genome of the strain Ligilactobacillus salivarius IBB3154 was sequenced, and transcriptome analysis was carried out at two different temperatures, allowing the determination of gene expression levels in response to environmental changes (temperature). Genes with higher expression at 42°C were identified. The use of a reporter gene (β- glucuronidase) did not confirm the transcriptomic results; it was found that the promoters of the genes sasA1 and sasA2 were active in the presence of bile salts. This opens up new opportunities for the overexpression of genes of other bacterial species in Ligilactobacillus cells in the intestinal environment.
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Affiliation(s)
- Patrycja Kobierecka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Agnieszka Wyszyńska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Agnieszka Sałańska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jacek Bardowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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81
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Wang Y, Shang P, Dai Y, Xu D, Dong Y, Huang Z. The complete mitochondrial genome of a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). Mitochondrial DNA B Resour 2023; 8:1356-1359. [PMID: 38196799 PMCID: PMC10776055 DOI: 10.1080/23802359.2023.2288437] [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: 05/21/2023] [Accepted: 11/21/2023] [Indexed: 01/11/2024] Open
Abstract
Schizothorax gulinensis sp. nov. is a new species of the genus Schizothorax from Sichuan, China (Cypriniformes: Cyprinidae). In this study, we have first reported the complete mitochondrial genome of S. gulinensis with Illumina sequencing. There were 16,587 nucleotide pairs in the mitochondrial genome (mitogenome) of S. gulinensis, including 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs), as well as one non-coding control region (CR). The proportion of nucleotides in mitochondrial genome was 29.67% (A), 25.45% (T), 17.84% (G), 27.05% (C), and A + T content was 55.12%. All PCGs have the same start codon of the standard ATG, excepting for that of NADH dehydrogenase subunit 1 (nad1) which was the ATC, NADH dehydrogenase subunit 5 (nad5) which was the ATT and cytochrome c oxidase 1 (cox1) which was the ATC. Phylogenetic analysis results supported that S. gulinensis was closely related to Schizothorax grahami. The complete mitochondrial sequence of S. gulinensis will contribute to mitochondrial genome database and provide useful resources for population genetics and evolution analyses.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Pan Shang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai, PR China
| | - Yuanxing Dai
- Gulin County Bureau of Agriculture and Rural Affairs, Luzhou, PR China
| | - Dayong Xu
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Yanzhen Dong
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
| | - Zhiqiu Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang, PR China
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82
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Girijan SK, Pillai D, Devika R. Complete genome sequence analysis of multi-drug resistant Klebsiella pneumoniae THK strain isolated from aquaculture farm in Kerala, India. 3 Biotech 2023; 13:394. [PMID: 37970451 PMCID: PMC10643474 DOI: 10.1007/s13205-023-03820-8] [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: 03/22/2023] [Accepted: 10/11/2023] [Indexed: 11/17/2023] Open
Abstract
The emergence of microorganisms with resistance toward antibiotics has been widely recognized as a growing hazard to public health. Here, we report the whole genome sequence of Klebsiella pneumoniae strain THK, which was isolated from an aquaculture farm in Kerala, India. Standard disc diffusion and strip methods were used for antibiotic susceptibility testing and minimum inhibitory concentration detection. The isolate showed high level of resistance against beta-lactam, aminoglycosides, fluoroquinolones, macrolides, tetracyclines, chloramphenicol, sulfonamides, and cephalosporin class of antibiotics, but were sensitive to carbapenem and polymyxins. The whole genome sequence analysis revealed that the final assembly of THK strain consisted of 30 contigs of 5, 199,186 bp including four plasmid sequences plasmid_690 (1 contig), plasmid_710 (9 contigs), plasmid_1222 (6 contigs), and plasmid_1528 (1 contig). Sequence analysis revealed that the isolate has a number of genes encoding for antibiotic resistance and virulence. The findings indicated that antibiotics present in aquatic environments at sub-inhibitory concentrations increase the selection pressure affecting the cell function of even normal aquatic microorganisms to change the genetic expression of virulence factors or acquire resistance genes through various transfer mechanisms. This strain would be of significant interest for thorough comparative genomic study, given the known vast diversity of pathogenic and antibiotic resistance potentials.
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Affiliation(s)
- Sneha Kalasseril Girijan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, Kerala India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, Kerala India
| | - Raj Devika
- National Institute of Oceanography, Regional Centre, Kochi, Kerala India
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83
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Yang HW, Thapa R, Johnson K, DuPont ST, Khan A, Zhao Y. Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types. PHYTOPATHOLOGY 2023; 113:2174-2186. [PMID: 36935376 DOI: 10.1094/phyto-01-23-0004-sa] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
| | - Ranjita Thapa
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Kenneth Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | | | - Awais Khan
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
- Department of Plant Pathology, WSU-IAREC, Prosser, WA 99350
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He M, Zhang L, Hu H, Liu X, Zhang C, Xin Y, Liu B, Chen Z, Xu K, Liu Y. Complete genome sequencing and comparative genomic analyses of a new spotted-fever Rickettsia heilongjiangensis strain B8. Emerg Microbes Infect 2023; 12:2153085. [PMID: 36440590 PMCID: PMC9930820 DOI: 10.1080/22221751.2022.2153085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rickettsia heilongjiangensis, a tick-borne obligate intracellular bacterium and causative agent of spotted fever in China, has attracted increasing concern regarding its capability in causing human rickettsiosis. Here, we conducted a genomic analysis of a new R. heilongjiangensis strain B8 (B8) isolated from the serum of a patient who had been bitten by a Haemaphysalis longicornis tick in Anhui Province, China. The present study sought to identify exclusive genes that might be associated with the pathogenicity of B8 using comparative genomics. Specifically, the sequences of B8 were assembled into one circular chromosome of 1,275,081 bp and predicted to contain 1447 genes. Comparative genome analyses were performed based on the genome of B8 and 28 spotted fever group (SFG) rickettsial genomes deposited in NCBI. Phylogenomic analyses indicated the B8 strain was clustered within the R. heilongjiangensis species; however, a sum of 112 and 119 B8-unique genes was identified when compared with R. heilongjiangensis and R. japonica strains, respectively. Functional annotation analyses revealed that these B8-unique genes were mainly annotated to defence mechanisms, lipid transport and metabolism, cell wall/membrane/envelope biogenesis. These data indicate B8 rather represents a previously undescribed human-pathogenic SFG rickettsia lineage, which may be an intermediate lineage of R. heilongjiangensis and R. japonica. Overall, this study isolated a new strain of R. heilongjiangensis in East-Central China for the first time, and provided potential B8-unique genetic loci that could be used for the discrimination of B8 from other R. heilongjiangensis and closely related SFG Rickettsial strains.
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Affiliation(s)
- Maozhang He
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Lifeng Zhang
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Haoran Hu
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Xiaohan Liu
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Cong Zhang
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Yu Xin
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Boyu Liu
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Zhen Chen
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China
| | - Kehan Xu
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China,Kehan Xu Department of Microbiology, School of Basic Medical, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, No. 81 Meishan Road, Hefei, Anhui230032, People’s Republic of China
| | - Yan Liu
- Department of Microbiology, School of Basic Medical; The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, Anhui Medical University, Hefei, People’s Republic of China, Yan Liu
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85
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Hassan MA, Tan Z, Shen R, Xing J. Comparative mitochondrial genome analysis of three leafhopper species of the genus Abrus Dai & Zhang (Hemiptera: Cicadellidae: Deltocephalinae) from China with phylogenetic implication. BMC Genomics 2023; 24:714. [PMID: 38012556 PMCID: PMC10680345 DOI: 10.1186/s12864-023-09809-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND The phylogenetic position and classification of Athysanini are poorly defined, as it includes a large group of polyphyletic genera that have historically been assigned to it mainly because they still exhibit the most typical deltocephaline genitalic and external body characters but lack the distinctive characteristics that other tribes possess. The bamboo-feeding leafhopper genus Abrus belong to the tribe Athysanini of subfamily Deltocephalinae, which currently comprises 19 valid described species, and are limited to the Oriental and Palaearctic regions in China. Although the taxonomy of Abrus are well updated, the references on comparative mitogenomic analyses of Abrus species are only known for a single species. In this study, we sequenced and analyzed the complete mitochondrial genomes (mitogenomes) of Abrus daozhenensis Chen, Yang & Li, 2012 (16,391bp) and A. yunshanensis Chen, Yang & Li, 2012 (15,768bp) (Athysanini), and compared with published mitogenome sequence of A. expansivus Xing & Li, 2014 (15,904bp). RESULTS These Abrus species shared highly conserved mitogenomes with similar gene order to that of the putative ancestral insect with 37 typical genes and a non-coding A + T-rich region. The nucleotide composition of these genomes is highly biased toward A + T nucleotides (76.2%, 76.3%, and 74.7%), AT-skews (0.091 to 0.095, and 0.095), negative GC-skews (- 0.138, - 0.161, and - 0.138), and codon usage. All 22 tRNA genes had typical cloverleaf secondary structures, except for trnS1 (AGN) which lacks the dihydrouridine arm, and distinctively trnG in the mitogenome of A. expansivus lacks the TψC arm. Phylogenetic analyses based on 13 PCGs, 2 rRNA genes, and 22 tRNA genes consistently recovered the monophyletic Opsiini, Penthimiini, Selenocephalini, Scaphoideini, and Athysanini (except Watanabella graminea, previously sequenced species as Chlorotettix nigromaculatus) based on limited available mitogenome sequence data of 37 species. CONCLUSION At present, Abrus belongs to the tribe Athysanini based on both morphological and molecular datasets, which is strongly supported in present phylogenetic analyses in both BI and ML methods using the six concatenated datasets: amino acid sequences and nucleotides from different combinations of protein-coding genes (PCGs), ribosomal RNA (rRNAs), and transfer RNA (tRNAs). Phylogenetic trees reconstructed herein based on the BI and ML analyses consistently recovered monophylitic Athysanini, except Watanabella graminea (Athysanini) in Opsiini with high support values.
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Affiliation(s)
- Muhammad Asghar Hassan
- Institute of Entomology, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Zhixiang Tan
- Institute of Entomology, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Rongrong Shen
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152, USA
| | - Jichun Xing
- Institute of Entomology, The Provincial Special Key Laboratory for Development and Utilization of Insect Resources, Guizhou University, Guiyang, 550025, Guizhou, China.
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86
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Chiou YJ, Chan YF, Yu SP, Lu CY, Hsiao SSY, Chiang PW, Hsu TC, Liu PY, Wada N, Lee Y, Jane WN, Lee DC, Huang YW, Tang SL. Similar but different: Characterization of dddD gene-mediated DMSP metabolism among coral-associated Endozoicomonas. SCIENCE ADVANCES 2023; 9:eadk1910. [PMID: 37992165 PMCID: PMC10664990 DOI: 10.1126/sciadv.adk1910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Endozoicomonas are often predominant bacteria and prominently important in coral health. Their role in dimethylsulfoniopropionate (DMSP) degradation has been a subject of discussion for over a decade. A previous study found that Endozoicomonas degraded DMSP through the dddD pathway. This process releases dimethyl sulfide, which is vital for corals coping with thermal stress. However, little is known about the related gene regulation and metabolic abilities of DMSP metabolism in Endozoicomonadaceae. In this study, we isolated a novel Endozoicomonas DMSP degrader and observed a distinct DMSP metabolic trend in two phylogenetically close dddD-harboring Endozoicomonas species, confirmed genetically by comparative transcriptomic profiling and visualization of the change of DMSP stable isotopes in bacterial cells using nanoscale secondary ion spectrometry. Furthermore, we found that DMSP cleavage enzymes are ubiquitous in coral Endozoicomonas with a preference for having DddD lyase. We speculate that harboring DMSP degrading genes enables Endozoicomonas to successfully colonize various coral species across the globe.
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Affiliation(s)
- Yu-Jing Chiou
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Fan Chan
- Department of Microbiology, Soochow University, Taipei 111, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | | | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Ting-Chang Hsu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Liu
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Wann-Neng Jane
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Der-Chuen Lee
- Institute of Astronomy and Astrophysics, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Wen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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87
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Han W, Feng D, Dai S. Characterization of the complete mitochondrial genome of a forensically important beetle, Ptomascopus plagiatus (Coleoptera: staphylinidae: silphinae). Mitochondrial DNA B Resour 2023; 8:1276-1279. [PMID: 38188433 PMCID: PMC10769529 DOI: 10.1080/23802359.2023.2281705] [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: 02/22/2023] [Accepted: 10/17/2023] [Indexed: 01/09/2024] Open
Abstract
Ptomascopus plagiatus (Ménétriés, 1854) is a forensically important silphid species. In this study, we report on the mitochondrial genome of P. plagiatus. The complete mitochondrial genome of P. plagiatus is 17556 bp and contains 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and a 2953 bp noncoding region. The nucleotide composition of P. plagiatus is biased toward A and T (A + T: 77.46%). Phylogenetic analysis based on mitogenomic data supports that P. plagiatus is closely related to (Nicrophorus nepalensis Hope, 1831 + Nicrophorus vespilloides Herbst, 1783) within the subfamily Silphinae.
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Affiliation(s)
- Wei Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, China
| | - Dianxing Feng
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, China
| | - Shutong Dai
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, China
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88
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Dutta B, Halder U, Chitikineni A, Varshney RK, Bandopadhyay R. Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention. BMC Genomics 2023; 24:681. [PMID: 37957573 PMCID: PMC10642018 DOI: 10.1186/s12864-023-09764-w] [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: 06/01/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others. RESULTS Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences. CONCLUSION The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain's adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.
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Affiliation(s)
- Bhramar Dutta
- Department of Botany, Microbiology Section, The University of Burdwan, Burdwan, West, Bengal-713104, India
| | - Urmi Halder
- Department of Botany, Microbiology Section, The University of Burdwan, Burdwan, West, Bengal-713104, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6500, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, 6500, Australia
| | - Rajib Bandopadhyay
- Department of Botany, Microbiology Section, The University of Burdwan, Burdwan, West, Bengal-713104, India.
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89
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Cantillo Villa Y, Triga A, Katharios P. Polyinfection in Fish Aeromoniasis: A Study of Co-Isolated Aeromonas Species in Aeromonas veronii Outbreaks. Pathogens 2023; 12:1337. [PMID: 38003801 PMCID: PMC10674900 DOI: 10.3390/pathogens12111337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
We studied the phenotypic and genomic characteristics related to the virulence and antibiotic resistance of two Aeromonas strains, which were co-isolated before an outbreak of Aeromonas veronii among diseased seabass on Agathonisi Island, Greece, in April 2015. The first strain, AG2.13.2, is a potentially pathogenic mesophilic variant of Aeromonas salmonicida, and the second, AG2.13.5, corresponds to an Aeromonas rivipollensis related to A. rivipollensis KN-Mc-11N1 with an ANI value of 97.32%. AG2.13.2 lacks the type III secretion system just like other mesophilic strains of A. salmonicida. This characteristic has been associated with lower virulence. However, the genome of AG2.13.2 contains other important virulence factors such as type II and type VI secretion systems, and toxins such as rtxA, aerolysin aer/act, and different types of hemolysins. The strain also carries several genes associated with antibiotic resistance such as the tetE efflux pump, and exhibits resistance to tetracycline, ampicillin, and oxolinic acid. In an in vivo challenge test with gilthead seabream larvae, the A. veronii bv sobria strain AG5.28.6 exhibited the highest virulence among all tested strains. Conversely, both A. salmonicida and A. rivipollensis showed minimal virulence when administered alone. Interestingly, when A. veronii bv sobria AG5.28.6 was co-administered with A. rivipollensis, the larvae survival probability increased compared to those exposed to A. veronii bv sobria AG5.28.6 alone. This finding indicates an antagonistic interaction between A. veronii bv sobria AG5.28.6 and A. rivipollensis AG2.13.5. The co-administration of A. veronii bv sobria AG5.28.6 with Aeromonas salmonicida did not yield distinct survival probabilities. Our results validate that the primary pathogen responsible for European seabass aeromoniasis is Aeromonas veronii bv sobria.
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Affiliation(s)
- Yanelys Cantillo Villa
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Adriana Triga
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Department of Biology, University of Crete, 71110 Heraklion, Greece
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), 71500 Gournes, Greece; (Y.C.V.); (A.T.)
- Aquatic Biologicals, Thalassocosmos, 71500 Gournes, Greece
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90
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Wang C, Ye P, Pillans R, Chen X, Wang J, Feutry P. Evolution of the Critically Endangered Green Sawfish Pristis zijsron (Rhinopristiformes, Pristidae), Inferred from the Whole Mitochondrial Genome. Genes (Basel) 2023; 14:2052. [PMID: 38002995 PMCID: PMC10671267 DOI: 10.3390/genes14112052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The green sawfish Pristis zijsron (Bleeker, 1851), a species of sawfish in the family Pristidae (Rhinopristiformes), mainly inhabits the Indo-West Pacific region. In this study, the complete mitochondrial genome of the critically endangered green sawfish is first described. The length of the genome is 16,804 bp, with a nucleotide composition of 32.0% A, 24.8% C, 13.1% G, and 30.0% T. It contains 37 genes in the typical gene order of fish. Two start (GTG and ATG) and two stop (TAG and TAA/T-) codons are found in the thirteen protein-coding genes. The 22 tRNA genes range from 67 bp (tRNA-Ser) to 75 bp (tRNA-Leu). The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicates that the family Pristidae are suffering a purifying selection. The reconstruction of Bayesian inference and the maximum likelihood phylogenetic tree show the same topological structure, and the family Pristidae is a monophyletic group with strong posterior probability. Pristis zijsron and P. pectinata form a sister group in the terminal clade. And the divergence time of Rhinopristiformes show that P. zijsron and P. pectinata diverged as two separate species in about Paleogene 31.53 Mya. Complete mitochondrial genomes of all five sawfishes have been published and phylogenetic relationships have been analyzed. The results of our study will provide base molecular information for subsequent research (e.g., distribution, conservation, phylogenetics, etc.) on this endangered group.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361000, China;
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Peiyuan Ye
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Richard Pillans
- CSIRO Environment, Boggo Road, Dutton Park, QLD 4102, Australia;
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; (P.Y.); (X.C.)
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Pierre Feutry
- CSIRO Environment, Castray Esplanade, Hobart, TAS 7000, Australia
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Voronina OL, Kunda MS, Ryzhova NN, Aksenova EI, Kustova MA, Karpova TI, Melkumyan AR, Klimova EA, Gruzdeva OA, Tartakovsky IS. Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates. Life (Basel) 2023; 13:2167. [PMID: 38004307 PMCID: PMC10672678 DOI: 10.3390/life13112167] [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: 09/13/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Listerias of the phylogenetic lineage II (PLII) are common in the European environment and are hypovirulent. Despite this, they caused more than a third of the sporadic cases of listeriosis and multi-country foodborne outbreaks. L. monocytogenes ST37 is one of them. During the COVID-19 pandemic, ST37 appeared in clinical cases and ranked second in occurrence among food isolates in the Moscow region. The aim of this study was to describe the genomic features of ST37 isolates from different sources. All clinical cases of ST37 were in the cohort of male patients (age, 48-81 years) with meningitis-septicemia manifestation and COVID-19 or Influenza in the anamnesis. The core genomes of the fish isolates were closely related. The clinical and meat isolates revealed a large diversity. Prophages (2-4/genome) were the source of the unique genes. Two clinical isolates displayed pseudolysogeny, and excided prophages were A006-like. In the absence of plasmids, the assortment of virulence factors and resistance determinants in the chromosome corresponded to the hypovirulent characteristics. However, all clinical isolates caused severe disease, with deaths in four cases. Thus, these studies allow us to speculate that a previous viral infection increases human susceptibility to listeriosis.
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Affiliation(s)
- Olga L. Voronina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Marina S. Kunda
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Natalia N. Ryzhova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Ekaterina I. Aksenova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Margarita A. Kustova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Tatiana I. Karpova
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
| | - Alina R. Melkumyan
- F.I. Inosemtsev City Clinical Hospital, Fortunatovskaya Str., 1, 105187 Moscow, Russia;
| | - Elena A. Klimova
- Department of Infectious Diseases and Epidemiology, A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Ministry of Health of the Russian Federation, Delegatskaya Str., 20, Building 1, 127473 Moscow, Russia;
| | - Olga A. Gruzdeva
- Federal State Budgetary Educational Institution of Further Professional Education Russian Medical Academy of Continuous Professional Education, Ministry of Health of the Russian Federation, Barrikadnaya Str., 2/1, Building 1, 125993 Moscow, Russia;
| | - Igor S. Tartakovsky
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya Str., 18, 123098 Moscow, Russia; (M.S.K.); (N.N.R.); (E.I.A.); (M.A.K.); (T.I.K.); (I.S.T.)
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Liu M, Hu R, Xia M, He X, Jin Y. Novel broad-spectrum bacteriophages against Xanthomonas oryzae and their biocontrol potential in rice bacterial diseases. Environ Microbiol 2023; 25:2075-2087. [PMID: 37300421 DOI: 10.1111/1462-2920.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Bacterial leaf blight (BLB) and bacterial leaf streak (BLS)-caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively-are two major bacterial diseases that threaten the safe production of rice, one of the most important food crops. Bacteriophages are considered potential biocontrol agents against rice bacterial pathogens, due to their host specificity and environmental safety. It is common for BLB and BLS to occur together in fields, which highlights the need for broad-spectrum phages capable of infecting both Xoo and Xoc. In this study, two lytic broad-spectrum phages (pXoo2106 and pXoo2107) that can infect various strains of Xoo and Xoc were assessed. Both phages belong to the class Caudoviricetes and one of them to the family Autographiviridae, while the other belongs to an unclassified family. Two phages alone or combined in a phage cocktail could effectively inhibit Xoo and Xoc growth in vitro. In an in vivo biocontrol experiment, the phage cocktail reduced the total CFU and significantly eased the symptoms caused by Xoo or Xoc. Our results suggest that pXoo2106 and pXoo2107 have a broad-spectrum host range targeting different X. oryzae strains, and have strong biocontrol potential in field applications against both BLB and BLS.
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Affiliation(s)
- Mengjiao Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Ran Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Mian Xia
- Hainan Yazhou Bay Seed Laboratory, Hainan, China
| | - Xiaoqing He
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, China
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93
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Zhang Y, Lv F, Su Y, Zhang H, Zhang B. Complete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates. Front Microbiol 2023; 14:1285027. [PMID: 38029076 PMCID: PMC10646407 DOI: 10.3389/fmicb.2023.1285027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery. Methods Three S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes. Results Whole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains. Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase. Discussion In summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.
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Affiliation(s)
| | | | - Yan Su
- Department of Microbiology and Immunology, College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, Xinjiang, China
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94
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Huq MA, Rahman MS, Rahman MM, Akter S. Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction. Int J Syst Evol Microbiol 2023; 73. [PMID: 37937829 DOI: 10.1099/ijsem.0.006136] [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: 11/09/2023] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.
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Affiliation(s)
- Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia-7003, Bangladesh
| | - Shahina Akter
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 461-701, Republic of Korea
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95
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Hu J, Li YH, Liu J, Xu Z, Wu HB, Cheng C, Chu XD, Wu ZD. The complete mitochondrial genome of Rhinogobius maculagenys (Gobiidae:Gobionellinae). Mitochondrial DNA B Resour 2023; 8:1141-1144. [PMID: 38188428 PMCID: PMC10769551 DOI: 10.1080/23802359.2023.2274617] [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: 06/27/2023] [Accepted: 10/18/2023] [Indexed: 01/09/2024] Open
Abstract
The complete mitochondrial genome of Rhinogobius maculagenys Wu et al., (Perciformes,Gobiidae) was sequenced and annotated in this study. The circular mitogenome is 16,500 bp long and consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and two main non-coding regions (a putative control region and an L-strand replication origin). The overall base composition is 27.5% A, 25.5% T, 16.9% G, and 30.1% C. The gene order and composition are similar to those of other Gobionellinae species. Phylogenetic analysis revealed that R. maculagenys is closely related to Rhinogobius shennongensis in both the maximum likelihood tree and the Bayesian inference tree. The complete mitogenome of R. maculagenys will serve as a valuable resource for future studies on evolution, taxonomy, and genetic conservation of Rhinogobius.
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Affiliation(s)
- Jia Hu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Yan-hua Li
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Jun Liu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Zhou Xu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Hai-Bing Wu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Chao Cheng
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Xu-Dong Chu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
| | - Zhang-Dong Wu
- Mianyang Academy of Agricultural Sciences, Mianyang, P.R. China
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96
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Zhou X, Lei Y, Dietrich CH, Huang M. Investigating Monophyly of Typhlocybini Based on Complete Mitochondrial Genomes with Characterization and Comparative Analysis of 19 Species (Hemiptera: Cicadellidae: Typhlocybinae). INSECTS 2023; 14:842. [PMID: 37999041 PMCID: PMC10671860 DOI: 10.3390/insects14110842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Tribes of the leafhopper subfamily Typhlocybinae have traditionally been defined based on differences in forewing and hindwing venation. Except for Typhlocybini (sensu lato), the classification of tribes is relatively stable. The monophyly of Typhlocybini needs to be examined, and the relationships among genera within Typhlocybini have not been resolved. Few mitogenome sequences representative of major lineages of Typhlocybini have been available to facilitate a comprehensive phylogenetic analysis of the tribe. In this study, the complete mitogenomes of 19 species of Typhlocybini were sequenced. The gene arrangements of the 19 new mitogenomes are consistent with ancestral insect mitogenomes. Phylogenetic analyses by both maximum-likelihood and Bayesian methods of 67 species of Typhlocybinae suggest that Zyginellini is paraphyletic with respect to Typhlocybini. The phylogenetic relationships within Typhlocybini are discussed, and the major results show that the Farynala and Linnavuoriana complexes previously recognized based on morphological characters correspond to monophyletic lineages.
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Affiliation(s)
- Xian Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
| | - Yuejie Lei
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
| | - Christopher H. Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S. Oak St., Champaign, IL 61820, USA;
| | - Min Huang
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Entomological Museum, College of Plant Protection, Northwest A&F University, Xianyang 712100, China; (X.Z.); (Y.L.)
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97
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Fatima A, Ibrahim M, Naseer A, Pervez A, Asad M, Shah AA, Hasan F, Alonazi WB, Ferheen I, Khan S. Identification, Genome Sequencing, and Characterizations of Helicobacter pylori Sourced from Pakistan. Microorganisms 2023; 11:2658. [PMID: 38004670 PMCID: PMC10673187 DOI: 10.3390/microorganisms11112658] [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: 09/24/2023] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
The stomach's colonization by Helicobacter pylori (H. pylori) results in gastritis, ulcers, and stomach cancer. Frequently, pain is treated with medication, but resistant H. pylori infections are not. Therefore, it is important to find pharmacological targets and improved treatments for resistant H. pylori strains. The aim of the current study was sampling, identification, drug susceptibility testing following genome sequencing and comparative genome-wide analysis of selected H. pylori strains from Pakistan with three representative strains for virulence and drug-resistant characteristics. Based on culture, biochemistry, and molecular biology, 84 strains of H. pylori were identified, which made up 47% of the enrolled cases. Among all H. pylori strains, the highest resistance was reported for metronidazole with 82 H. pylori strains (98%), followed by clarithromycin with 62 resistant strains (74%). Among metronidazole-resistant strains, 38 strains (46%) were also resistant to clarithromycin, contributing 61% of clarithromycin resistant cases. Two strains, HPA1 and HPA2, isolated from 'gastritis' and 'gastric ulcer' patients, respectively, were further processed for WGS. The draft genome sequences of H. pylori strains HPA1 and HPA2 encode 1.66 Mbp and 1.67 Mbp genome size, 24 and 4 contiguous DNA sequences, and 1650 and 1625 coding sequences, respectively. Both the genomes showed greater than 90% similarity with the reference strain H. pylori ATCC 43504/PMSS1. The antibiotic-resistant genes were identified among all the strains with overall similarity above 95%, with minor differences in the sequence similarity. Using the virulent gene data obtained from the Virulence Factor Database, 75 to 85 virulent genes were identified in the five genome assemblies with various key genes such as cytolethal distending toxin (cdt), type IV secretion system, cag PAI, plasticity region, cell-motility- and flagellar-associated genes, neutrophil-activating protein (HP-NAP), T4SS effector cytotoxin-associated gene A (cagA), and urease-associated genes ureA and ureB, etc. Sequence similarity between the virulence factors found in this study and reference genes was at least 90%. In summary, the results of our study showed the relationship between clinical results and specific H. pylori strains' (HPA1 and HPA2) genetics such as antibiotic resistance and specific virulence factors. These findings provide valued understanding of the epidemiology of H. pylori-associated diseases. Moreover, identification and genomics analysis have provided insights into the epidemiology, genetic diversity, pathogenicity, and potential drug resistance genes of H. pylori strains, offering a foundation for developing more targeted and effective medical interventions, including anti-virulent medications.
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Affiliation(s)
- Anees Fatima
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
- Department of Microbiology, Faculty of Health & Biological Sciences, Abbottabad University of Science & Technology, Abbottabad 22500, Pakistan
| | - Muhammad Ibrahim
- Department of Biosciences, COMSATS University Islamabad (CUI), Sahiwal Campus, Sahiwal 55000, Pakistan (M.A.)
| | - Adil Naseer
- Department of Gastroenterology, Ayub Medical College, Main Mansehra Road, Abbottabad 22020, Pakistan;
| | - Arshid Pervez
- Department of Environmental Sciences, COMSATS University Islamabad (CUI), Abbottabad Campus, University Road, Tobe Camp, Abbottabad 22010, Pakistan;
| | - Muhammad Asad
- Department of Biosciences, COMSATS University Islamabad (CUI), Sahiwal Campus, Sahiwal 55000, Pakistan (M.A.)
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
| | - Fariha Hasan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
| | - Wadi B. Alonazi
- Health Administration Department, College of Business Administration, King Saud University, Riyadh 11587, Saudi Arabia;
| | - Ifra Ferheen
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Samiullah Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan; (A.F.); (A.A.S.); (F.H.)
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98
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Zheng J, Li F, Fan M, Gu Z, Liu C, Wang A, Yang Y. Mitogenomic Phylogeny of Tonnoidea Suter, 1913 (1825) (Gastropoda: Caenogastropoda). Animals (Basel) 2023; 13:3342. [PMID: 37958096 PMCID: PMC10649890 DOI: 10.3390/ani13213342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/01/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The Tonnoidea Suter, 1913 (1825) is a moderately diverse group of large predatory gastropods, the systematics of which remain unclear. In the present study, the complete mitochondrial genomes of nine Tonnoidean species were sequenced. All newly sequenced mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, showing similar patterns in genome size, gene order and nucleotide composition. The ratio of nonsynonymous to synonymous of PCGs indicated that NADH complex genes of Tonnoideans were experiencing a more relaxed purifying selection compared with the COX genes. The reconstructed phylogeny based on the combined amino acid sequences of 13 protein-coding genes and the nucleotide sequences of two rRNA genes supported that Ficidae Meek, 1864 (1840) is a sister to Tonnoidea. The monophylies of all Tonnoidean families were recovered and the internal phylogenetic relationships were consistent with the current classification. The phylogeny also revealed that Tutufa rebuta (Linnaeus, 1758) is composed of at least two different species, indicating that the species diversity within Bursidae Thiele, 1925 might be underestimated. The present study contributes to the understanding of the Tonnoidean systematics, and it could provide important information for the revision of Tonnoidean systematics in the future.
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Affiliation(s)
- Jiawen Zheng
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Fengping Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Mingfu Fan
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Zhifeng Gu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Chunsheng Liu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Aimin Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
| | - Yi Yang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; (J.Z.); (F.L.); (M.F.); (Z.G.); (C.L.); (A.W.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
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99
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Cheng HY, Gao QI, Pan Z. Mitochondrial genomes of three Mylabris (Pseudabris) species (Coleoptera: Meloidae, Mylabrini) and their phylogenetic implications. Zootaxa 2023; 5357:186-204. [PMID: 38220647 DOI: 10.11646/zootaxa.5357.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Indexed: 01/16/2024]
Abstract
The complete mitogenomes of the subgenus Mylabris (Pseudabris) Fairmaire, 1894, endemic to the Qinghai-Xizang Plateau, are reported for the first time. Three species out of seven, M. hingstoni Blair, 1927, M. longiventris Blair, 1927, and M. przewalskyi (Dokhtouroff, 1887), were sequenced. The sequencing results of mitogenomes were annotated and analyzed. The gene arrangements were consistent with the putative ancestral insect mitogenomes as understood today, including 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a noncoding internal control region (CR). The PCGs used the typical start ATN codon and TAA/TAG stop codons. The lengths of three mitogenomes were 15,692 bp, 15,685 bp, and 15,685 bp, with an A + T content of 71.29%, 71.67%, and 71.53%, respectively. The evolution rates of 13 PCGs were compared: The evolution rate of ATP8 was the highest, and that of COX1 was the lowest. Furthermore, the phylogenetic relationships among the genera and tribes of Meloidae were discussed.
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Affiliation(s)
- Hai-Yun Cheng
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
| | - Q I Gao
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
| | - Zhao Pan
- Key Laboratory of Zoological Systematics and Application; School of Life Sciences; Institute of Life Science and Green Development; Hebei University; Wusidong Road 180; 071002; Baoding; Hebei Province; China.
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100
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Shrestha P, Karmacharya J, Han SR, Lee JH, Oh TJ. Elucidation of cold adaptation in Glaciimonas sp. PAMC28666 with special focus on trehalose biosynthesis. Front Microbiol 2023; 14:1280775. [PMID: 37920266 PMCID: PMC10618363 DOI: 10.3389/fmicb.2023.1280775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Glaciimonas sp. PAMC28666, an extremophilic bacterium thriving in Antarctic soil and belonging to the Oxalobacteraceae family, represents the only complete genome of its genus available in the NCBI database. Its genome measures 5.2 Mb and comprises 4,476 genes (4,350 protein-coding and 72 non-coding). Phylogenetic analysis shows the strain PAMC28666 in a unique branch within the genus Glaciimonas, closely related to Glaciimonas alpine Cr9-12, supported by robust bootstrap values. In addition, strain PAMC28666 showed 77.08 and 23.3% ANI and DDH, respectively, with Glaciimonas sp. PCH181.This study focuses on how polar strain PAMC28666 responds to freeze-thaw conditions, Experimental results revealed a notable survival rate of 47.28% when subjected to a temperature of 15°C for a period of 10 days. Notably, two genes known to be responsive to cold stress, Trehalose 6-phosphate synthase (otsA) and Trehalose 6-phosphate phosphatase (otsB), exhibited increased expression levels as the temperature shifted from 25°C to 15°C. The upregulation of otsAB and the consequent synthesis of trehalose play pivotal roles in enhancing the cold resistance of strain PAMC28666, offering valuable insights into the correlation between trehalose production and adaptation to cold stress. Furthermore, research into this neglected cold-adapted variation, like Glaciimonas sp. PAMC28666, has the potential to shed light on how trehalose is produced in cold-adapted environments Additionally, there is potential to extract trehalose compounds from this strain for diverse biotechnological applications, including food and cosmetics, with ongoing research exploring its unique properties.
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Affiliation(s)
- Prasansah Shrestha
- Department of Life Sciences and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - Jayram Karmacharya
- Department of Life Sciences and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Department of Life Sciences and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based Bio-IT Convergence Institute, Asan, Republic of Korea
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Materials, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Sciences and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based Bio-IT Convergence Institute, Asan, Republic of Korea
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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