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11 "Comparative genomics"
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Journal Article
Genomic Characterization and Comparative Analysis of Streptococcus zhangguiae sp. nov. Isolated from the Respiratory Tract of Marmota Himalayana
Caixin Yang, Jiajia Ma, Huimin Zhou, Jing Yang, Ji Pu, Shan Lu, Dong Jin, Liyun Liu, Kui Dong, Jianguo Xu
J. Microbiol. 2024;62(11):951-963.   Published online November 4, 2024
DOI: https://doi.org/10.1007/s12275-024-00177-2
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AbstractAbstract
Two Gram-stain-positive, oxidase-negative, non-motile, facultative anaerobic, α-hemolytic, coccus-shaped bacteria (zg-86T and zg-70) were isolated from the respiratory tracts of marmots (Marmota Himalayana) on the Qinghai-Tibet Plateau of China. Phylogenetic analysis of the 16S rRNA gene and 545 core genes revealed that these two strains belong to the Streptococcus genus. These strains were most closely related to Streptococcus respiraculi HTS25T, Streptococcus cuniculi CCUG 65085T, and Streptococcus marmotae HTS5T. The average nucleotide identity (ANI) and digital DNA‒DNA hybridization (dDDH) were below the threshold for species delineation. The predominant cellular fatty acids (CFAs) in this novel species were C16:0, C18:0, and C18:1ω9c, whereas the primary polar lipids were phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and an unknown phosphoglycolipid (PGL). The optimal growth conditions for the strains were 37 °C, pH 7.0, and 0.5% (w/v) NaCl on brain-heart infusion (BHI) agar supplemented with 5% defibrinated sheep blood. Comparative genomics analyses revealed the potential pathogenicity of strain zg-86T through comparisons with suis subclade strains in terms of virulence factors, pathogen-host interactions (PHIs) and mobile genetic factors (MGEs). Based on the phenotypic characteristics and phylogenetic analyses, we propose that these two isolates represent novel species in the genus Streptococcus, for which the names Streptococcus zhangguiae sp. nov. (the type strain zg-86T=GDMCC 1.1758T=JCM 34273T) is proposed.
Review
Extensive Genomic Rearrangement of Catalase-Less Cyanobloom-Forming Microcystis aeruginosa in Freshwater Ecosystems
Minkyung Kim, Jaejoon Jung, Wonjae Kim, Yerim Park, Che Ok Jeon, Woojun Park
J. Microbiol. 2024;62(11):933-950.   Published online October 8, 2024
DOI: https://doi.org/10.1007/s12275-024-00172-7
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AbstractAbstract
Many of the world's freshwater ecosystems suffer from cyanobacteria-mediated blooms and their toxins. However, a mechanistic understanding of why and how Microcystis aeruginosa dominates over other freshwater cyanobacteria during warmer summers is lacking. This paper utilizes comparative genomics with other cyanobacteria and literature reviews to predict the gene functions and genomic architectures of M. aeruginosa based on complete genomes. The primary aim is to understand this species' survival and competitive strategies in warmer freshwater environments. M. aeruginosa strains exhibiting a high proportion of insertion sequences (~ 11%) possess genomic structures with low synteny across different strains. This indicates the occurrence of extensive genomic rearrangements and the presence of many possible diverse genotypes that result in greater population heterogeneities than those in other cyanobacteria in order to increase survivability during rapidly changing and threatening environmental challenges. Catalase-less M. aeruginosa strains are even vulnerable to low light intensity in freshwater environments with strong ultraviolet radiation. However, they can continuously grow with the help of various defense genes (e.g., egtBD, cruA, and mysABCD) and associated bacteria. The strong defense strategies against biological threats (e.g., antagonistic bacteria, protozoa, and cyanophages) are attributed to dense exopolysaccharide (EPS)-mediated aggregate formation with efficient buoyancy and the secondary metabolites of M. aeruginosa cells. Our review with extensive genome analysis suggests that the ecological vulnerability of M. aeruginosa cells can be overcome by diverse genotypes, secondary defense metabolites, reinforced EPS, and associated bacteria.
Journal Articles
Saxibacter everestensis gen. nov., sp. nov., A Novel Member of the Family Brevibacteriaceae, Isolated from the North Slope of Mount Everest
Mao Tian, Shiyu Wu, Wei Zhang, Gaosen Zhang, Xue Yu, Yujie Wu, Puchao Jia, Binglin Zhang, Tuo Chen, Guangxiu Liu
J. Microbiol. 2024;62(4):277-284.   Published online March 6, 2024
DOI: https://doi.org/10.1007/s12275-024-00108-1
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AbstractAbstract
We isolated and analyzed a novel, Gram-stain-positive, aerobic, rod-shaped, non-motile actinobacterium, designated as strain ZFBP1038(T), from rock sampled on the north slope of Mount Everest. The growth requirements of this strain were 10-37 °C, pH 4-10, and 0-6% (w/v) NaCl. The sole respiratory quinone was MK-9, and the major fatty acids were anteiso-C(15:0) and iso-C(17:0). Peptidoglycan containing meso-diaminopimelic acid, ribose, and glucose were the major cell wall sugars, while polar lipids included diphosphatidyl glycerol, phosphatidyl glycerol, an unidentified phospholipid, and an unidentified glycolipid. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ZFBP1038(T) has the highest similarity with Spelaeicoccus albus DSM 26341( T) (96.02%). ZFBP1038(T) formed a distinct monophyletic clade within the family Brevibacteriaceae and was distantly related to the genus Spelaeicoccus. The G + C content of strain ZFBP1038(T) was 63.65 mol% and the genome size was 4.05 Mb. Digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between the genomes of strain ZFBP1038(T) and representative reference strains were 19.3-25.2, 68.0-71.0, and 52.8-60.1%, respectively. Phylogenetic, phenotypic, and chemotaxonomic characteristics as well as comparative genome analyses suggested that strain ZFBP1038(T) represents a novel species of a new genus, for which the name Saxibacter gen. nov., sp. nov. was assigned with the type strain Saxibacter everestensis ZFBP1038(T) (= EE 014( T) = GDMCC 1.3024( T) = JCM 35335( T)).
Impact of Elevational Gradients and Chemical Parameters on Changes in Soil Bacterial Diversity Under Semiarid Mountain Region
Salman Khan , Chun Han , Awais Iqbal , Chao Guan , Changming Zhao
J. Microbiol. 2023;61(10):903-915.   Published online November 23, 2023
DOI: https://doi.org/10.1007/s12275-023-00085-x
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AbstractAbstract
Elevation gradients, often regarded as “natural experiments or laboratories”, can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We obtained bacterial sequences using MiSeq sequencing and clustered them into operational taxonomic units (OTUs). The total number of reads obtained by the bacterial 16S rRNA sequencing analysis was 1,090,555, with an average of approximately 45,439 reads per sample collected from various elevations. The current study observed inconsistent bacterial diversity patterns in samples from the lowest to highest elevations. 983 OTUs were found common among all the elevations. The most unique OTUs were found in the soil sample from elevation_2, followed by elevation_1. Soil sample collected at elevation_6 had the least unique OTUs. Actinobacteria, Protobacteria, Chloroflexi were found most abundant bacterial phyla in current study. Ammonium nitrogen ( NH4 +-N), and total phosphate (TP) are the main factors influencing bacterial diversity at elevations_ 1. pH was the main factor influencing the bacterial diversity at elevations_2, elevation_3 and elevation_4. Our results provide new visions on forming and maintaining soil microbial diversity along an elevational gradient and have implications for microbial responses to environmental change in semiarid mountain ecosystems.
Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish
Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae
J. Microbiol. 2022;60(6):576-584.   Published online April 18, 2022
DOI: https://doi.org/10.1007/s12275-022-1604-3
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  • 5 Web of Science
  • 6 Crossref
AbstractAbstract
Three aerobic, Gram-negative, and rod-shaped bacterial strains, designated strains G4M1T, SM13T, and L12M9T, were isolated from the gut of Batillaria multiformis, Cellana toreuma, and Patinopecten yessoensis collected from the Yellow Sea in South Korea. All the strains grew optimally at 25°C, in the presence of 2% (w/v) NaCl, and at pH 7. These three strains, which belonged to the genus Polaribacter in the family Flavobacteriaceae, shared < 98.8% in 16S rRNA gene sequence and < 86.68% in whole-genome sequence with each other. Compared with the type strains of Polaribacter, isolates showed the highest sequence similarity to P. haliotis KCTC 52418T (< 98.68%), followed by P. litorisediminis KCTC 52500T (< 98.13%). All the strains contained MK-6 as their predominant menaquinone and iso-C15:0 as their major fatty acid. Moreover, all the strains had phosphatidylethanolamine as their polar lipid component. In addition, strain G4M1T had two unidentified lipids and three unidentified aminolipids, strain SM13T had three unidentified lipids and three unidentified aminolipids, and strain L12M9T had three unidentified lipids and one unidentified aminolipid. The DNA G + C contents of strains G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%, respectively. Based on phenotypic, phylogenetic, chemotaxonomic, and genotypic findings, strains G4M1T (= KCTC 82388T = DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T), and L12M9T (= KCTC 62751T = DSM 112374T) were classified into the genus Polaribacter as the type strains of novel species, for which the names Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., respectively, have been proposed.

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  • Unique skin microbiome: insights to understanding bacterial symbionts in octopuses
    Chelsea O. Bennice, Lauren E. Krausfeldt, W. Randy Brooks, Jose V. Lopez
    Frontiers in Marine Science.2024;[Epub]     CrossRef
  • An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
    Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
    Journal of Clinical Microbiology.2024;[Epub]     CrossRef
  • Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013
    Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon
    International Journal of Systematic and Evolutionary Microbiology .2024;[Epub]     CrossRef
  • Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
    Meora Rajeev, Jang-Cheon Cho
    Journal of Microbiology.2024; 62(11): 985.     CrossRef
  • Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, George Garrity
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
  • Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
    Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
    International Journal of Systematic and Evolutionary Microbiology .2022;[Epub]     CrossRef
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh , Joon Yong Kim , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi
J. Microbiol. 2021;59(5):460-466.   Published online April 28, 2021
DOI: https://doi.org/10.1007/s12275-021-0513-1
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AbstractAbstract
To date, all species in the genus Salicibibacter have been isolated in Korean commercial kimchi. We aimed to describe the taxonomic characteristics of two strains, NKC5-3T and NKC21-4T, isolated from commercial kimchi collected from various regions in the Republic of Korea. Cells of these strains were rod-shaped, Gram-positive, aerobic, oxidase- and catalase- positive, non-motile, halophilic, and alkalitolerant. Both strains, unlike other species of the genus Salicibibacter, could not grow without NaCl. Strains NKC5-3T and NKC21-4T could tolerate up to 25.0% (w/v) NaCl (optimum 10%) and grow at pH 7.0–10.0 (optimum 8.5) and 8.0–9.0 (optimum 8.5), respectively; they showed 97.1% 16S rRNA gene sequence similarity to each other and were most closely related to S. kimchii NKC1-1T (97.0% and 96.8% similarity, respectively). The genome of strain NKC5-3T was nearly 4.6 Mb in size, with 4,456 protein-coding sequences (CDSs), whereas NKC21-4T genome was nearly 3.9 Mb in size, with 3,717 CDSs. OrthoANI values between the novel strains and S. kimchii NKC1-1T were far lower than the species demarcation threshold. NKC5-3T and NKC21-4T clustered together to form branches that were distinct from the other Salicibibacter species. The major fatty acids in these strains were anteiso-C15:0 and anteiso-C17:0, and the predominant menaquinone was menaquinone-7. The polar lipids of NKC5-3T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and five unidentified phospholipids (PL), and those of NKC21-4T included DPG, PG, seven unidentified PLs, and an unidentified lipid. Both isolates had DPG, which is the first case in the genus Salicibibacter. The genomic G + C content of strains NKC5-3T and NKC21-4T was 44.7 and 44.9 mol%, respectively. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic analyses, strains NKC5-3T (= KACC 22040T = DSM 111417T) and NKC21-4T (= KACC 22041T = DSM 111418T) represent two novel species of the genus Salicibibacter, for which the names Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov. are proposed.

Citations

Citations to this article as recorded by  
  • Valid publication of new names and new combinations effectively published outside the IJSEM
    Aharon Oren, George M. Garrity
    International Journal of Systematic and Evolutionary Microbiology .2021;[Epub]     CrossRef
Role of melatonin in murine “restraint stress”-induced dysfunction of colonic microbiota
Rutao Lin , Zixu Wang , Jing Cao , Ting Gao , Yulan Dong , Yaoxing Chen
J. Microbiol. 2021;59(5):500-512.   Published online February 25, 2021
DOI: https://doi.org/10.1007/s12275-021-0305-7
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  • 13 Web of Science
  • 15 Crossref
AbstractAbstract
Intestinal diseases caused by physiological stress have become a severe public health threat worldwide. Disturbances in the gut microbiota-host relationship have been associated with irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory and antioxidant effects. The objective of this study was to investigate the mechanisms by which MT-mediated protection mitigated stress-induced intestinal microbiota dysbiosis and inflammation. We successfully established a murine restraint stress model with and without MT supplementation. Mice subjected to restraint stress had significantly elevated corticosterone (CORT) levels, decreased MT levels in their plasma, elevated colonic ROS levels and increased bacterial abundance, including Bacteroides and Tyzzerella, in their colon tract, which led to elevated expression of Toll-like receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation with 20 mg/kg MT reversed the elevation of the plasma CORT levels, downregulated the colon ROS levels and inhibited the changes in the intestinal microbiota induced by restraint stress. These effects, in turn, inhibited the activities of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory reaction induced by restraint stress. Our results suggested that MT may mitigate “restraint stress”-induced colonic microbiota dysbiosis and intestinal inflammation by inhibiting the activation of the NF-κB pathway.

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    Biomedicine & Pharmacotherapy.2024; 180: 117377.     CrossRef
  • The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective
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    The Journal of Physiology.2023; 601(20): 4491.     CrossRef
  • Melatonin as a Mediator of the Gut Microbiota–Host Interaction: Implications for Health and Disease
    María-Ángeles Bonmatí-Carrión, Maria-Angeles Rol
    Antioxidants.2023; 13(1): 34.     CrossRef
  • INVESTIGATION OF THE ROLE OF STRESS IN MALE INFERTILITY AND THE EFFECT OF CURRENT MELATONIN HORMONE TREATMENTS
    İshak GÖKÇEK, Leyla AYDIN
    Veteriner Farmakoloji ve Toksikoloji Derneği Bülteni.2023; 14(1): 36.     CrossRef
  • The double burden of malnutrition and environmental enteric dysfunction as potential factors affecting gut-derived melatonin in children under adverse environments
    Alane N. Bezerra, Caroline L. Peixoto, Synara C. Lopes, Veralice M. S. Bruin, Pedro Felipe C. Bruin, Reinaldo B. Oriá
    Frontiers in Nutrition.2023;[Epub]     CrossRef
  • Melatonin: Both a Messenger of Darkness and a Participant in the Cellular Actions of Non-Visible Solar Radiation of Near Infrared Light
    Dun-Xian Tan, Russel J. Reiter, Scott Zimmerman, Ruediger Hardeland
    Biology.2023; 12(1): 89.     CrossRef
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    Ichiro Chihara, Hiromitsu Negoro, Jin Kono, Yoshiyuki Nagumo, Haruki Tsuchiya, Kosuke Kojo, Masanobu Shiga, Ken Tanaka, Shuya Kandori, Bryan J. Mathis, Hiroyuki Nishiyama
    Communications Biology.2023;[Epub]     CrossRef
  • The Microbiota-Dependent Worsening Effects of Melatonin on Gut Inflammation
    Jefferson Luiz da Silva, Lia Vezenfard Barbosa, Camila Figueiredo Pinzan, Viviani Nardini, Irislene Simões Brigo, Cássia Aparecida Sebastião, Jefferson Elias-Oliveira, Vânia Brazão, José Clóvis do Prado Júnior, Daniela Carlos, Cristina Ribeiro de Barros C
    Microorganisms.2023; 11(2): 460.     CrossRef
  • The Effects of Stress and Diet on the “Brain–Gut” and “Gut–Brain” Pathways in Animal Models of Stress and Depression
    Mauritz F. Herselman, Sheree Bailey, Larisa Bobrovskaya
    International Journal of Molecular Sciences.2022; 23(4): 2013.     CrossRef
  • Intestinal microbiota and melatonin in the treatment of secondary injury and complications after spinal cord injury
    Yiwen Zhang, Rui Lang, Shunyu Guo, Xiaoqin Luo, Huiting Li, Cencen Liu, Wei Dong, Changshun Bao, Yang Yu
    Frontiers in Neuroscience.2022;[Epub]     CrossRef
  • Protective Effects and Mechanisms of Melatonin on Stress Myocardial Injury in Rats
    Jia-yao Chen, Ting Li, Jiao-ling Wang, Zhan-le Wang, Yun Zhang, Lin-quan Zang
    Journal of Cardiovascular Pharmacology.2022; 80(3): 417.     CrossRef
  • Rescue of social deficits by early-life melatonin supplementation through modulation of gut microbiota in a murine model of autism
    Xia Liu, Yi Cui, Yuhan Zhang, Guo Xiang, Meng Yu, Xianshu Wang, Bin Qiu, Xin-gang Li, Wei Liu, Di Zhang
    Biomedicine & Pharmacotherapy.2022; 156: 113949.     CrossRef
  • Roles of PRR-Mediated Signaling Pathways in the Regulation of Oxidative Stress and Inflammatory Diseases
    Pengwei Li, Mingxian Chang
    International Journal of Molecular Sciences.2021; 22(14): 7688.     CrossRef
Monthly distribution of ammonia-oxidizing microbes in a tropical bay
Tie-Qiang Mao , Yan-Qun Li , Hong-Po Dong , Wen-Na Yang , Li-Jun Hou
J. Microbiol. 2021;59(1):10-19.   Published online November 17, 2020
DOI: https://doi.org/10.1007/s12275-021-0287-5
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AbstractAbstract
Ammonia oxidation, performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), plays a critical role in the cycle of nitrogen in the ocean. For now, environmental variables controlling distribution of ammonia-oxidizing microbes are still largely unknown in oceanic environments. In this study, we used real-time quantitative PCR and high-throughput sequencing
methods
to investigate the abundance and diversity of AOA and AOB from sediment and water in Zhanjiang Bay. Phylogenic analysis revealed that the majority of AOA amoA sequences in water and sediment were affiliated with the genus Nitrosopumilus, whereas the Nitrosotalea cluster was only detected with low abundance in water. Nitrosomonas and Nitrosospira dominated AOB amoA sequences in water and sediment, respectively. The amoA copy numbers of both AOA and AOB varied significantly with month for both sediment and water. When water and sediment temperature dropped to 17– 20°C in December and February, respectively, the copy number of AOB amoA genes increased markedly and was much higher than for AOA amoA genes. Also, AOA abundance in water peaked in December when water temperature was lowest (17–20°C). Stepwise multiple regression analyses revealed that temperature was the most key factor driving monthly changes of AOA or AOB abundance. It is inferred that low water temperature may inhibit growth of phytoplankton and other microbes and so reduce competition for a common substrate, ammonium.
Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation
Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha
J. Microbiol. 2018;56(11):798-804.   Published online October 24, 2018
DOI: https://doi.org/10.1007/s12275-018-8372-0
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  • 21 Crossref
AbstractAbstract
The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.

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    Yuting Li, Peng Gu, Wen Zhang, Hongwen Sun, Jianing Wang, Leilei Wang, Bing Li, Lei Wang
    Journal of Hazardous Materials.2023; 449: 131001.     CrossRef
  • Recent trends in polycyclic aromatic hydrocarbons pollution distribution and counteracting bio-remediation strategies
    Selvaraj Barathi, Gitanjali J, Gandhimathi Rathinasamy, Nadana Sabapathi, K.N. Aruljothi, Jintae Lee, Sabariswaran Kandasamy
    Chemosphere.2023; 337: 139396.     CrossRef
  • Evaluation of the Different Nutritional and Environmental Parameters on Microbial Pyrene Degradation by Mangrove Culturable Bacteria
    Manzoor Ahmad, Juan Ling, Jianping Yin, Luxiang Chen, Qingsong Yang, Weiguo Zhou, Yuhang Zhang, Xiaofang Huang, Imran Khan, Junde Dong
    International Journal of Molecular Sciences.2023; 24(9): 8282.     CrossRef
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    Arfin Imam, Sunil Kumar Suman, Pankaj K. Kanaujia, Anjan Ray
    Bioresource Technology.2022; 343: 126121.     CrossRef
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    Ilaria Gabriele, Marco Race, Stefano Papirio, Patrizia Papetti, Giovanni Esposito
    Chemosphere.2022; 300: 134578.     CrossRef
  • A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix
    Mohammad Qutob, Mohd Rafatullah, Syahidah Akmal Muhammad, Abeer M. Alosaimi, Hajer S. Alorfi, Mahmoud A. Hussein
    Fermentation.2022; 8(6): 260.     CrossRef
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    Sergey N. Golubev, Anna Yu. Muratova, Leonid V. Panchenko, Sergey Yu. Shchyogolev, Olga V. Turkovskaya
    Microbiological Research.2021; 253: 126885.     CrossRef
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    Xinjiao Dong, Yaru Li, Rui Zhu, Chuanhua Wang, Shimei Ge
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Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism
Man-Young Jung , So-Jeong Kim , Jong-Geol Kim , Heeji Hong , Joo-Han Gwak , Soo-Je Park , Yang-Hoon Kim , Sung-Keun Rhee
J. Microbiol. 2018;56(5):365-371.   Published online May 2, 2018
DOI: https://doi.org/10.1007/s12275-018-7451-6
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AbstractAbstract
Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H+ and Na+ ions, respectively. Strain IRF9 harbored two different types of ATPases (Na+-dependent F-type ATPase and H+- dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions.

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Review
The Use of the Rare UUA Codon to Define "Expression Space" for Genes Involved in Secondary Metabolism, Development and Environmental Adaptation in Streptomyces
Keith F. Chater , Govind Chandra
J. Microbiol. 2008;46(1):1-11.
DOI: https://doi.org/10.1007/s12275-007-0233-1
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AbstractAbstract
In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2~3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor-it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.

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