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Amara Y, Mahjoubi M, Souissi Y, Cherif H, Naili I, ElHidri D, Kadidi I, Mosbah A, Masmoudi AS, Cherif A. Tapping into haloalkaliphilic bacteria for sustainable agriculture in treated wastewater: insights into genomic fitness and environmental adaptation. Antonie Van Leeuwenhoek 2024; 118:1. [PMID: 39269515 DOI: 10.1007/s10482-024-02012-5] [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: 02/08/2024] [Accepted: 08/16/2024] [Indexed: 09/15/2024]
Abstract
The increasing salinity and alkalinity of soils pose a global challenge, particularly in arid regions such as Tunisia, where about 50% of lands are sensitive to soil salinization. Anthropogenic activities, including the use of treated wastewater (TWW) for irrigation, exacerbate these issues. Haloalkaliphilic bacteria, adapted to TWW conditions and exhibiting plant-growth promotion (PGP) and biocontrol traits, could offer solutions. In this study, 24 haloalkaliphilic bacterial strains were isolated from rhizosphere sample of olive tree irrigated with TWW for more than 20 years. The bacterial identification using 16S rRNA gene sequencing showed that the haloalkaliphilic isolates, capable of thriving in high salinity and alkaline pH, were primarily affiliated to Bacillota (Oceanobacillus and Staphylococcus). Notably, these strains exhibited biofertilization and enzyme production under both normal and saline conditions. Traits such as phosphate solubilization, and the production of exopolysaccharide, siderophore, ammonia, and hydrogen cyanide were observed. The strains also demonstrated enzymatic activities, including protease, amylase, and esterase. Four selected haloalkaliphilic PGPR strains displayed antifungal activity against Alternaria terricola, with three showing tolerances to heavy metals and pesticides. The strain Oceanobacillus picturea M4W.A2 was selected for genome sequencing. Phylogenomic analyses indicated that the extreme environmental conditions probably influenced the development of specific adaptations in M4W.A2 strain, differentiating it from other Oceanobacillus picturae strains. The presence of the key genes associated with plant growth promotion, osmotic and oxidative stress tolerance, antibiotic and heavy metals resistance hinted the functional capabilities might help the strain M4W.A2 to thrive in TWW-irrigated soils. By demonstrating this connection, we aim to improve our understanding of genomic fitness to stressed environments. Moreover, the identification of gene duplication and horizontal gene transfer events through mobile genetic elements allow the comprehension of these adaptation dynamics. This study reveals that haloalkaliphilc bacteria from TWW-irrigated rhizosphere exhibit plant-growth promotion and biocontrol traits, with genomic adaptations enabling their survival in high salinity and alkaline conditions, offering potential solutions for soil salinization issues.
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Affiliation(s)
- Yosra Amara
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
- National Agronomy Institute of Tunisia, Avenue Charles Nicolle, 1082, Tunis, Mahrajène, Tunisia
| | - Mouna Mahjoubi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Yasmine Souissi
- Department of Engineering, German University of Technology in Oman, P.O. Box 1816, 130, Muscat, Oman
| | - Hanene Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Islem Naili
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Darine ElHidri
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Imen Kadidi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Amor Mosbah
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Ahmed S Masmoudi
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Ameur Cherif
- Univ. Manouba, ISBST, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia.
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Yang S, Han X, Li J, Luan F, Zhang S, Han D, Yang M, Chen Q, Qi Z. Oceanobacillus picturae alleviates cadmium stress and promotes growth in soybean seedlings. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134568. [PMID: 38749246 DOI: 10.1016/j.jhazmat.2024.134568] [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: 03/18/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Cadmium (Cd) is a heavy metal that significantly impacts human health and the environment. Microorganisms play a crucial role in reducing heavy metal stress in plants; however, the mechanisms by which microorganisms enhance plant tolerance to Cd stress and the interplay between plants and microorganisms under such stress remain unclear. In this study, Oceanobacillus picturae (O. picturae) was isolated for interaction with soybean seedlings under Cd stress. Results indicated that Cd treatment alone markedly inhibited soybean seedling growth. Conversely, inoculation with O. picturae significantly improved growth indices such as plant height, root length, and fresh weight, while also promoting recovery in soil physiological indicators and pH. Metabolomic and transcriptomic analyses identified 157 genes related to aspartic acid, cysteine, and flavonoid biosynthesis pathways. Sixty-three microbial species were significantly associated with metabolites in these pathways, including pathogenic, adversity-resistant, and bioconductive bacteria. This research experimentally demonstrates, for the first time, the growth-promoting effect of the O. picturae strain on soybean seedlings under non-stress conditions. It also highlights its role in enhancing root growth and reducing Cd accumulation in the roots under Cd stress. Additionally, through the utilization of untargeted metabolomics, metagenomics, and transcriptomics for a multi-omics analysis, we investigated the impact of O. picturae on the soil microbiome and its correlation with differential gene expression in plants. This innovative approach unveils the molecular mechanisms underlying O. picturae's promotion of root growth and adaptation to Cd stress.
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Affiliation(s)
- Shangjun Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Xue Han
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Jun Li
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Feng Luan
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang 163000, China
| | - Shuli Zhang
- Wuchang Branch of Heilongjiang Academy of Agricultural Sciences, Wuchang, Heilongjiang 150229, People's Republic of China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, China
| | - Mingliang Yang
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Qingshan Chen
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
| | - Zhaoming Qi
- National Research Center of Soybean Engineering and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Liu W, Nan F, Liu F, Yang X, Li Z, Jiang S, Zhang X, Li J, Yu M, Wang Y, Wang B. Isolation and identification of uric acid-dependent Aciduricibacillus chroicocephali gen. nov., sp. nov. from seagull feces and implications for hyperuricemia treatment. mSphere 2024; 9:e0002524. [PMID: 38814072 PMCID: PMC11332149 DOI: 10.1128/msphere.00025-24] [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: 01/10/2024] [Accepted: 04/10/2024] [Indexed: 05/31/2024] Open
Abstract
Hyperuricemia has become the second most prevalent metabolic disease after diabetes, but the limitations of urate-lowering treatment (ULT) drugs and patient nonadherence make ULT far less successful. Thus, more ULT approaches urgently need to be explored. Uric acid-degrading bacteria have potential application value in ULT. In this study, we isolated 44XBT, a uric acid-degrading bacterium, from black-headed gull (Chroicocephalus ridibundus) feces. Using a polyphasic taxonomic approach, strain 44XBT was identified as a novel genus within the family Bacillaceae; subsequently, the name Aciduricibacillus chroicocephali was proposed. Strain 44XBT had a unique uric acid-dependent phenotype and utilized uric acid and allantoin as the sole carbon and nitrogen sources, but not common carbon sources or complex media. In the genome, multiple copies of genes involved in uric acid metabolic pathway (pucL, pucM, uraD, and allB) were found. Six copies of pucL (encoding urate oxidase) were detected. Of these, five pucL copies were in a tandem arrangement and shared 70.42%-99.70% amino acid identity. In vivo experiments revealed that 44XBT reduced serum uric acid levels and attenuated kidney damage in hyperuricemic mice through uric acid catalysis in the gut and gut microbiota remodeling. In conclusion, our findings discover a strain for studying bacterial uric acid metabolism and may provide valuable insights into ULT. IMPORTANCE The increasing disease burden of hyperuricemia highlights the need for new therapeutic drugs and treatment strategies. Our study describes the developmental and application values of natural uric acid-degrading bacteria found in the gut of birds and broadened the source of bacteria with potential therapeutic value. Furthermore, the special physiology characteristics and genomic features of strain 44XBT are valuable for further study.
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Affiliation(s)
- Wenxuan Liu
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Fulong Nan
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Fengjun Liu
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaoli Yang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Zonghui Li
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shasha Jiang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xianjuan Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jun Li
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Meng Yu
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yunyang Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bin Wang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
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Miliotis G, Sengupta P, Hameed A, Chuvochina M, McDonagh F, Simpson AC, Parker CW, Singh NK, Rekha PD, Morris D, Raman K, Kyrpides NC, Hugenholtz P, Venkateswaran K. Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio 2024; 15:e0018124. [PMID: 38477597 PMCID: PMC11005411 DOI: 10.1128/mbio.00181-24] [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: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive microbial surveillance was conducted at NASA's Mars 2020 spacecraft assembly facility (SAF), where whole-genome sequencing (WGS) of 110 bacterial strains was performed. One isolate, designated 179-BFC-A-HST, exhibited less than 80% average nucleotide identity (ANI) to known species, suggesting a novel organism. This strain demonstrated high-level resistance [minimum inhibitory concentration (MIC) >256 mg/L] to third-generation cephalosporins, including ceftazidime, cefpodoxime, combination ceftazidime/avibactam, and the fourth-generation cephalosporin cefepime. The results of a comparative genomic analysis revealed that 179-BFC-A-HST is most closely related to Virgibacillus halophilus 5B73CT, sharing an ANI of 78.7% and a digital DNA-DNA hybridization (dDDH) value of 23.5%, while their 16S rRNA gene sequences shared 97.7% nucleotide identity. Based on these results and the recent recognition that the genus Virgibacillus is polyphyletic, strain 179-BFC-A-HST is proposed as a novel species of a novel genus, Tigheibacillus jepli gen. nov., sp. nov (type strain 179-BFC-A-HST = DSM 115946T = NRRL B-65666T), and its closest neighbor, V. halophilus, is proposed to be reassigned to this genus as Tigheibacillus halophilus comb. nov. (type strain 5B73CT = DSM 21623T = JCM 21758T = KCTC 13935T). It was also necessary to reclassify its second closest neighbor Virgibacillus soli, as a member of a novel genus Paracerasibacillus, reflecting its phylogenetic position relative to the genus Cerasibacillus, for which we propose Paracerasibacillus soli comb. nov. (type strain CC-YMP-6T = DSM 22952T = CCM 7714T). Within Amphibacillaceae (n = 64), P. soli exhibited 11 antibiotic resistance genes (ARG), while T. jepli encoded for 3, lacking any known β-lactamases, suggesting resistance from variant penicillin-binding proteins, disrupting cephalosporin efficacy. P. soli was highly resistant to azithromycin (MIC >64 mg/L) yet susceptible to cephalosporins and penicillins. IMPORTANCE The significance of this research extends to understanding microbial survival and adaptation in oligotrophic environments, such as those found in SAF. Whole-genome sequencing of several strains isolated from Mars 2020 mission assembly cleanroom facilities, including the discovery of the novel species Tigheibacillus jepli, highlights the resilience and antimicrobial resistance (AMR) in clinically relevant antibiotic classes of microbes in nutrient-scarce settings. The study also redefines the taxonomic classifications within the Amphibacillaceae family, aligning genetic identities with phylogenetic data. Investigating ARG and virulence factors (VF) across these strains illuminates the microbial capability for resistance under resource-limited conditions while emphasizing the role of human-associated VF in microbial survival, informing sterilization practices and microbial management in similar oligotrophic settings beyond spacecraft assembly cleanrooms such as pharmaceutical and medical industry cleanrooms.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Pratyay Sengupta
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Anna C. Simpson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Punchappady D. Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, India
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Center for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Nikos C. Kyrpides
- US Department of Energy Joint Genome Institute, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Australia
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Basbas C, Garzon A, Schlesener C, van Heule M, Profeta R, Weimer BC, Silva-Del-Rio N, Byrne BA, Karle B, Aly SS, Lima FS, Pereira RV. Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome. Anim Microbiome 2023; 5:59. [PMID: 37986012 PMCID: PMC10662892 DOI: 10.1186/s42523-023-00281-5] [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: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge. RESULTS All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The α diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted < 0.01) in the diversity of genera between CT and MET samples (R2 = 0.112, P = 0.003) and a non-significant difference between MET and PUS samples (R2 = 0.036, P = 0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella. CONCLUSIONS The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased α-diversity but decreased β-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.
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Affiliation(s)
- Carl Basbas
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Adriana Garzon
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Cory Schlesener
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- 100K Pathogen Genome Project, University of California, Davis, CA, USA
| | - Machteld van Heule
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- Department of Morphology, Imaging, Orthopedics, Rehabilitation and Nutrition, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, Belgium
| | - Rodrigo Profeta
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Bart C Weimer
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- 100K Pathogen Genome Project, University of California, Davis, CA, USA
| | - Noelia Silva-Del-Rio
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Barbara A Byrne
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, USA
| | - Betsy Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, CA, USA
| | - Sharif S Aly
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Fabio S Lima
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Richard V Pereira
- Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA.
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Tong Y, Sun Q, Shao X, Wang Z. Effect of vaginal microbiota on pregnancy outcomes of women from Northern China who conceived after IVF. Front Endocrinol (Lausanne) 2023; 14:1200002. [PMID: 37547323 PMCID: PMC10400330 DOI: 10.3389/fendo.2023.1200002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/20/2023] [Indexed: 08/08/2023] Open
Abstract
Objective This study aimed to investigate the correlation between vaginal microbiota and pregnancy outcomes of women who achieved pregnancy via in vitro fertilization (IVF) in Northern China, and to determine a biomarker for evaluation of the risk of preterm births in these women. Methods In total, 19 women from Northern China women who conceived after IVF and 6 women who conceived naturally were recruited in this study. The vaginal samples of the healthy participants were collected throughout pregnancy, that is, during the first, second, and third trimesters. The V3-V4 region of 16S rRNA was used to analyze the vaginal microbiome, and the bioinformatic analysis was performed using QIIME Alpha and Beta diversity analysis. Results Either IVF group or Natural conception group, bacterial community diversities and total species number of vagnal samples from who delivered at term were significantly higher than those who delivered before term. Low abundance of vaginal bacteria indicates an increased risk of preterm delivery. Further, more abundant vaginal bacteria was found in first trimesters instead of the next two trimesters. Vignal samples collected during first trimester showed richer differences and more predictive value for pregnancy outcoes. In addition, the diversity of the vaginal bacterial community decreased as the gestational age increased, in all samples. Alloscardovia was only found in participants who conceived after IVF, and the percentage of Alloscardovia in viginal samples of normal delivery group is much higher than the samples from preterm delivery group.Vobrio specifically colonized in vagina of pregnant woman in AFT group (those who conceived after IVF (A), first trimester (F), and delivered at term (T)) and Sporosarcina was detected only in women with AFT and AST (those who conceived after IVF (A), second trimester (S), and delivered at term (T)). These data indicates that Alloscardovia, Vobrio and Sporosarcina have great potential in predicting pregnancy outcomes who pregnanted by vitro fertilization. Conclusions Vaginal microbiota were more stable in women who conceived naturally and those who carried pregnancy to term. Oceanobacillus might act as a positive biomarker, whereas Sulfurospirillum and Propionispira may act as negative biomarkers for the risk of preterm birth.
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Affiliation(s)
- Yu Tong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Obstetrics and Gynecology, Dalian Municipal Women and Children’s Medical Group, Dalian, Liaoning, China
| | - Qiang Sun
- Department of Obstetrics and Gynecology, Dalian Municipal Women and Children’s Medical Group, Dalian, Liaoning, China
| | - Xiaoguang Shao
- Department of Obstetrics and Gynecology, Dalian Municipal Women and Children’s Medical Group, Dalian, Liaoning, China
| | - Zhijian Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:2355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
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Zarei Jeliani Z, Sourinejad I, Afrand M, Shahdadi A, Yousefzadi M. Molecular Identification of Biofilm-Forming Marine Bacterial Strains Isolated from Different Substrates of Mangrove Habitat. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2022. [DOI: 10.1007/s40995-022-01383-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ren J, Deng L, Li C, Li Z, Dong L, Zhao J, Zhang J, Niu D. Evolution of antibiotic resistance genes and bacterial community during erythromycin fermentation residue composting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119746. [PMID: 35835274 DOI: 10.1016/j.envpol.2022.119746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 06/07/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The removal efficiency of antibiotic resistance genes (ARGs) is the biggest challenge for the treatment of erythromycin fermentation residue (EFR). In the current research, 0% (control), 10% (T1), and 30% (T2) spray-dried EFR were composted with bulking materials, consisting of cattle manure and maize straw, for 30 days. Environmental factors and bacterial community on the behaviors of ARGs were further investigated. Apart from the high levels of erythromycin, the electrical conductivities were also increased by 66.7% and 291.7% in the samples of T1 and T2, respectively. After 30 days of composting, total ARGs in the samples of control were decreased by 78.1%-91.2%, but those of T1 and T2 were increased 14.5-16.7- and 38.5-68.7-fold. ARGs related to ribosomal protection (erm) dominated the samples of T1 and T2 at D 13 and 30, especially that ermF accounted for more than 80% of the total ARGs. Furthermore, the results of bacterial community revealed that EFR promoted the growth of Proteobacteria and Bacteroidetes, but inhibited that of Actinobacteria, Verrucomicrobia and Chloroflexi. Network analysis revealed that the enriched ARGs had strong correlation with seven bacterial genera, including Halomonas, Oceanobacillus, and Alcaligenes, most of which are halotolerant. Above all, erythromycin combined with high salinity can have synergistic effect on the enrichment of ARGs and their hosts.
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Affiliation(s)
- Jianjun Ren
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, Changzhou 213164, China
| | - Liujie Deng
- State Environmental Protection Antibiotic Mycelial Dreg Harmless Treatment and Resource Utilization Engineering Technology Center, Yili Chuanning Biotechnology Co., Ltd., Yili 835007, China
| | - Chunyu Li
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, Changzhou 213164, China
| | - Zhijie Li
- State Environmental Protection Antibiotic Mycelial Dreg Harmless Treatment and Resource Utilization Engineering Technology Center, Yili Chuanning Biotechnology Co., Ltd., Yili 835007, China
| | - Liping Dong
- State Environmental Protection Antibiotic Mycelial Dreg Harmless Treatment and Resource Utilization Engineering Technology Center, Yili Chuanning Biotechnology Co., Ltd., Yili 835007, China
| | - Jian Zhao
- Department of Forensic Pathology, Guangzhou Forensic Science Institute and Key Laboratory of Forensic Pathology, Ministry of Public Security, Guangzhou 510000, China
| | - Jin Zhang
- Hebei Cixin Environmental Technology Co., Ltd., Langfang 065600, China
| | - Dongze Niu
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining, Changzhou University, Changzhou 213164, China.
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10
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Oceanobacillus saliphilus sp. nov., Isolated from Saline-Alkali Soil in Heilongjiang Province, China. Curr Microbiol 2022; 79:301. [PMID: 36002665 DOI: 10.1007/s00284-022-02997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 11/03/2022]
Abstract
A novel bacterium, designated strain APA_H-1(4)T, was isolated from the saline-alkaline soil, Zhaodong, Heilongjiang Province, China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus, and showed the highest sequence similarity to O. damuensis KCTC 33146T (98.35%, similarity) and 'O. massiliensis' DSM 24644 (98.32%). The average nucleotide identity values between strain APA_H-1(4)T and other members of the genus Oceanobacillus were lower than 82% recommended for distinguishing novel prokaryotic species. The digital DNA-DNA hybridization values of strain APA_H-1(4)T with O. damuensis KCTC 33146T and 'O. massiliensis' DSM 24644 were 13.60 and 17.60%, respectively. Cells of strain APA_H-1(4)T were Gram-staining positive, motile, aerobic, spore-forming rods (0.5-0.7 × 1.8-2.6 μm) with flagella. The growth was found to occur optimally at 37 °C. The whole-cell hydrolysate contained meso-diaminopimelic acid as the diagnostic cell wall diamino acid. The main detected polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified polar lipid. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). The major cellular fatty acid (>10%) was anteiso-C15:0. The G + C content of the genomic DNA was determined to be 38.4% based on the draft genome sequence. Based on the comparative analysis of polyphasic taxonomic data, strain APA_H-1(4)T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus saliphilus sp. nov. is proposed. The type strain is APA_H-1(4)T (=GDMCC 1.2239T = KCTC 43254T).
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11
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Jin PJ, Sun L, Rao MPN, Jiao JY, Sun XJ, Li WJ, Wang S. Oceanobacillus alkalisoli sp. nov., an alkaliphilic bacterium isolated from saline-alkaline soil. Int J Syst Evol Microbiol 2022; 72. [PMID: 36018779 DOI: 10.1099/ijsem.0.005518] [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: 09/26/2023] Open
Abstract
Two alkaliphilic strains, designated APA_J-2 (6-2)T and APA_J-5 (13-2), were isolated from saline-alkali soil sampled in Jilin Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains APA_J-2 (6-2)T and APA_J-5(13–2) were closely related to members of the genus
Oceanobacillus
, and had the highest sequence similarity to
Oceanobacillus indicireducens
JCM 17251T (96.8 and 96.9 %, respectively). The 16S rRNA gene sequence similarity between the two novel isolates was 99.6 %, indicating that they were similar species. Cells were Gram-stain-positive, aerobic, motile and rod-shaped. The strains grew at 15–45 °C (optimum, 37 °C), pH 8.0–11.0. (optimum, pH 9) and with 0–10 % (w/v) NaCl (optimum, 5 %). The strains contained menaquinone-7 as the respiratory quinone and anteiso-C15 : 0 as the predominant cellular fatty acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 40.0 mol%. The average nucleotide identity (ANI), amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values of strain APA_J-2 (6-2)T with
O. indicireducens
JCM 17251T were 85.5, 87.9 and 30.7 %, respectively. The ANI, AAI and dDDH values of strain APA_J-5 (13-2) with
O. indicireducens
JCM 17251T were 85.7, 87.7 and 30.8 %, respectively. Based on the phylogenetic, phenotypic, biochemical, chemotaxonomic and genome data, strains APA_J-2 (6-2)T and APA_J-5 (13-2) represent a novel species of the genus
Oceanobacillus
, for which the name Oceanobacillus alkalisoli sp. nov. is proposed. The type strain is APA_J-2 (6-2)T (=KCTC 43253T=GDMCC 1.2242T).
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Affiliation(s)
- Pin-Jiao Jin
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Lei Sun
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiu-Jun Sun
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Shuang Wang
- Heilongjiang Academy of Black Soil Conservation & Utilization, Postdoctoral Station of Heilongjiang Academy of Agricultural Sciences/ Key Lab of Soil Environment and Plant Nutrition of Heilongjiang Province/Heilongjiang Fertilizer Engineering Research Center, Harbin 150086, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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12
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Sieg J, Sandmeier CC, Lieske J, Meents A, Lemmen C, Streit WR, Rarey M. Analyzing structural features of proteins from deep-sea organisms. Proteins 2022; 90:1521-1537. [PMID: 35313380 DOI: 10.1002/prot.26337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 12/31/2022]
Abstract
Protein adaptations to extreme environmental conditions are drivers in biotechnological process optimization and essential to unravel the molecular limits of life. Most proteins with such desirable adaptations are found in extremophilic organisms inhabiting extreme environments. The deep sea is such an environment and a promising resource that poses multiple extremes on its inhabitants. Conditions like high hydrostatic pressure and high or low temperature are prevalent and many deep-sea organisms tolerate multiple of these extremes. While molecular adaptations to high temperature are comparatively good described, adaptations to other extremes like high pressure are not well-understood yet. To fully unravel the molecular mechanisms of individual adaptations it is probably necessary to disentangle multifactorial adaptations. In this study, we evaluate differences of protein structures from deep-sea organisms and their respective related proteins from nondeep-sea organisms. We created a data collection of 1281 experimental protein structures from 25 deep-sea organisms and paired them with orthologous proteins. We exhaustively evaluate differences between the protein pairs with machine learning and Shapley values to determine characteristic differences in sequence and structure. The results show a reasonable discrimination of deep-sea and nondeep-sea proteins from which we distinguish correlations previously attributed to thermal stability from other signals potentially describing adaptions to high pressure. While some distinct correlations can be observed the overall picture appears intricate.
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Affiliation(s)
- Jochen Sieg
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
| | | | - Julia Lieske
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | - Alke Meents
- Deutsches Elektronen-Synchrotron DESY, Center for Free-Electron Laser Science, Hamburg, Germany
| | | | - Wolfgang R Streit
- Universität Hamburg, Department of Microbiology and Biotechnology, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Hamburg, Germany
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13
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Zhao Y, Weng Q, Hu B. Microbial interaction promote the degradation rate of organic matter in thermophilic period. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 144:11-18. [PMID: 35299060 DOI: 10.1016/j.wasman.2022.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Composting is an efficient, microbe-driven method for the biodegradation of solid organic substrates. In such a complex engineering ecosystem, microbial interaction is more important to function than relative abundance and alpha diversity. However, microbial interaction and its driving force in the composting process has been rarely reported. Thus, we combined network analysis and positive cohesion to analyze the relationship between cooperation among bacteria taxa and the degradation of organic matter in ten industrial-scale food waste composting piles. The results showed that although the complexity of network and microbial diversity were inhibited by high temperature, microbial cooperation was stimulated in the thermophilic period. The positive cohesion, which reflected the degree of microbial cooperation, tended to be positively correlated with the degradation rate of organic matter, functional genera, and genes associated with organic matter degradation. Thus, microbial cooperation was a key factor in the promotion of the degradation of organic matter. From the insight microbial community, Thermobifida was the genera with high abundance, high occurrence frequency, and high contributions to microbial structure. Additionally, it was not only highly associated with the degree of cooperation but was also highly linked with the functional genera in the composting, implying that it might play an important role in regulating cooperation to promote the functional genera. Our research provides a deep understanding of the interaction among bacteria taxa during the composting process. Focusing on the abundance of Thermobifida might be an efficient way to improve composting quality by enhancing the cooperation of microbes.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Qin Weng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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14
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Kim M, Choi JH, Shin H, Lee WK, Byun JH. First Case of Bacteremia and Epididymo-orchitis Caused by Oceanobacillus oncorhynchi subspecies incaldanensis in an Immunocompetent Patient. Ann Lab Med 2022; 42:290-292. [PMID: 34635623 PMCID: PMC8548252 DOI: 10.3343/alm.2022.42.2.290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Mutbyul Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Jae Hwi Choi
- Department of Urology, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Hyoshim Shin
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Woo Kon Lee
- Department of Microbiology, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
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15
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Mohsin Bukhari S, Ahmed Alghamdi H, Ur Rehman K, Andleeb S, Ahmad S, Khalid N. Metagenomics analysis of the fecal microbiota in Ring-necked pheasants ( Phasianus colchicus) and Green pheasants ( Phasianus versicolor) using next generation sequencing. Saudi J Biol Sci 2022; 29:1781-1788. [PMID: 35280539 PMCID: PMC8913415 DOI: 10.1016/j.sjbs.2021.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022] Open
Abstract
Pheasant reintroduction and conservation efforts have been in place in Pakistan since the 1980 s, yet there is still a scarcity of data on pheasant microbiome and zoonosis. Instead of growing vast numbers of bacteria in the laboratory, to investigate the fecal microbiome, pheasants (green and ring neck pheasant) were analyzed using 16S rRNA metagenomics and using IonS5TMXL sequencing from two flocks more than 10 birds. Operational taxonomic unit (OTU) cluster analysis and phylogenetic tree analysis was performed using Mothur software against the SSUrRNA database of SILVA and the MUSCLE (Version 3.8.31) software. Results of the analysis showed that firmicutes were the most abundant phylum among the top ten phyla, in both pheasant species, followed by other phyla such as actinobacteria and proteobacteria in ring necked pheasant and bacteroidetes in green necked pheasant. Bacillus was the most relatively abundant genus in both pheasants followed by Oceanobacillus and Teribacillus for ring necked pheasant and Lactobacillus for green necked pheasant. Because of their well-known beneficial characteristics, these genus warrants special attention. Bird droppings comprise germs from the urinary system, gut, and reproductive sites, making it difficult to research each anatomical site at the same time. We conclude that metagenomic analysis and classification provides baseline information of the pheasant fecal microbiome that plays a role in disease and health.
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Affiliation(s)
- Syed Mohsin Bukhari
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Huda Ahmed Alghamdi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Khalil Ur Rehman
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahla Andleeb
- Department of Environmental Sciences, GCW University, Sailkot 51310, Pakistan
| | - Shahbaz Ahmad
- Department of Entomology, University of the Punjab, 54590 Lahore, Pakistan
| | - Nimra Khalid
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
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16
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Blandón LM, Marín MA, Quintero M, Jutinico-Shubach LM, Montoya-Giraldo M, Santos-Acevedo M, Gómez-León J. Diversity of cultivable bacteria from deep-sea sediments of the Colombian Caribbean and their potential in bioremediation. Antonie van Leeuwenhoek 2022; 115:421-431. [PMID: 35066712 DOI: 10.1007/s10482-021-01706-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/28/2021] [Indexed: 11/26/2022]
Abstract
The diversity of deep-sea cultivable bacteria was studied in seven sediment samples of the Colombian Caribbean. Three hundred and fifty two marine bacteria were isolated according to its distinct morphological character on the solid media, then DNA sequences of the 16S rRNA were amplified to identify the isolated strains. The identified bacterial were arranged in three phylogenetic groups, Firmicutes, Proteobacteria, and Actinobacteria, with 34 different OTUs defined at ≥ 97% of similarity and 70 OTUs at ≥ 98.65%, being the 51% Firmicutes, 34% Proteobacteria and 15% Actinobacteria. Bacillus and Fictibacillus were the dominant genera in Firmicutes, Halomonas and Pseudomonas in Proteobacteria and Streptomyces and Micromonospora in Actinobacteria. In addition, the strains were tested for biosurfactants and lipolytic enzymes production, with 120 biosurfactant producing strains (mainly Firmicutes) and, 56 lipolytic enzymes producing strains (Proteobacteria). This report contributes to the understanding of the diversity of the marine deep-sea cultivable bacteria from the Colombian Caribbean, and their potential application as bioremediation agents.
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Affiliation(s)
- Lina Marcela Blandón
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Mario Alejandro Marín
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas - UNICAMP, Campinas, SP, 13083-970, Brazil
| | - Marynes Quintero
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Laura Marcela Jutinico-Shubach
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Manuela Montoya-Giraldo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Marisol Santos-Acevedo
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia
| | - Javier Gómez-León
- Marine Bioprospecting Line, Marine and Coastal Research Institute "José Benito Vives de Andréis"- INVEMAR, Calle 25 No. 2-55, Playa Salguero, Santa Marta D.T.C.H., Colombia.
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17
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Li F, Yu H, Li Y, Wang Y, Shen Resource J, Hu D, Feng B, Han Y. The quality of compost was improved by low concentrations of fulvic acid owing to its optimization of the exceptional microbial structure. BIORESOURCE TECHNOLOGY 2021; 342:125843. [PMID: 34530250 DOI: 10.1016/j.biortech.2021.125843] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
The influence of different concentrations of fulvic acid at 0, 100, 200, and 400 mg/kg was evaluated during the course of composting with straw and mushroom residues as substrates. The optimal concentration of fulvic acid is 100 mg/Kg based on microbial characteristics, chemical parameters, and germination index testing. Nearly 80% of the microbial taxa responded significantly to fulvic acid over the composting period, with a dynamic change of the co-occurrence network from complex to simple and then to complex. Fulvic acid accelerated the progress of composting and reduced the emission of gases at the thermophilic phase. The optimal concentration of fulvic acid enriched the beneficial microorganisms Aeribacillus, Oceanobacillus, and Rhodospirillaceae, and decreased the abundances of pathogenic microorganisms Corynebacterium, Elizabethkingia, and Sarcocystidae. This study indicates a new strategy to optimize the composting process using the biostimulant fulvic acid.
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Affiliation(s)
- Fang Li
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Haiyou Yu
- Henan University of Animal Husbandry and Economy, Zhengzhou 450002, PR China
| | - Yue Li
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Yi Wang
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Jinwen Shen Resource
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Desheng Hu
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Biao Feng
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Yanlai Han
- College of Resources and Environment Science, Henan Agricultural University, Zhengzhou 450002, PR China.
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18
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Efficacy of a Next Generation Quaternary Ammonium Chloride Sanitizer on Staphylococcus and Pseudomonas Biofilms and Practical Application in a Food Processing Environment. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Foodborne pathogens are known to adhere strongly to surfaces and can form biofilms in food processing facilities; therefore, their potential to contaminate manufactured foods underscores the importance of sanitation. The objectives of this study were to (1) examine the efficacy of a new-generation sanitizer (Decon7) on Staphylococcus and Pseudomonas biofilms, (2) identify biofilm bacteria from workers’ boots in relation to previous sanitizer chemistry, (3) validate the efficacy of Decon7 on biofilm from workers’ boots from an abattoir/food processing environment, and (4) compare the sensitivity of isolated boot biofilm bacteria to new- and early (Bi-Quat)-generation QAC sanitizers. Decon7 was applied at two concentrations (5%, 10%) and was shown to be effective within 1 min of exposure against enhanced biofilms of Staphylococcus spp. and Pseudomonas spp. in 96-well microplates. Decon7 was also used to treat workers’ boots that had accumulated high levels of biofilm bacteria due to ineffective sanitization. Bacteria isolated before enzyme/sanitizer treatment were identified through 16S rRNA PCR and DNA sequencing. All treatments were carried out in triplicate and analyzed by one-way RM-ANOVA or ANOVA using the Holm–Sidak test for pairwise multiple comparisons to determine significant differences (p < 0.05). The data show a significant difference between Decon7 sanitizer treatment and untreated control groups. There was a ~4–5 log reduction in Staphylococcus spp. and Pseudomonas spp. (microplate assay) within the first 1 min of treatment and also a > 3-log reduction in the bacterial population observed in the biofilms from workers’ boots. The new next-generation QAC sanitizers are more effective than prior QAC sanitizers, and enzyme pre-treatment can facilitate biofilm sanitizer penetration on food contact surfaces. The rotation of sanitizer chemistries may prevent the selective retention of chemistry-tolerant microorganisms in processing facilities.
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Oceanobacillus salinisoli sp. nov., a bacterium isolated from saline soil of Turpan city in Xinjiang province, north-west China. Arch Microbiol 2021; 203:2919-2924. [PMID: 33763766 DOI: 10.1007/s00203-021-02287-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
YIM B00359T, a novel bacterial strain was isolated from the saline soil of Turpan city in Xinjiang province, north-west China. The strain was Gram-stain-positive, motile, aerobic, produced oval subterminal endospores in swollen sporangia. The whole-cell hydrolysates contain meso-diaminopimelic acid as the cell-wall diamino acid, with xylose, glucose, and ribose as the major whole-cell sugars. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids, and one unidentified glycophospholipid. The predominant menaquinone is MK-7. The major fatty acids are anteiso-C15:0, iso-C14:0, iso-C15:0, and iso-C16:0. The DNA G + C content of the type strain is 37.5 mol%. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus. However, it differed from its closest relatives, Oceanobacillus halophilus DSM 23996 T and Oceanobacillus senegalensis Marseille-P3587T in many physiological and chemotaxonomic characteristics. Based on comparative analysis of polyphasic taxonomic data, strain YIM B00359T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus salinisoli sp. nov. is proposed. The type strain is YIM B00359T (= CGMCC 1.17509T = KCTC 43185T).
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20
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Rodríguez-Gómez C, Durán-Riveroll LM, Okolodkov YB, Oliart-Ros RM, García-Casillas AM, Cembella AD. Diversity of Bacterioplankton and Bacteriobenthos from the Veracruz Reef System, Southwestern Gulf of Mexico. Microorganisms 2021; 9:619. [PMID: 33802890 PMCID: PMC8002828 DOI: 10.3390/microorganisms9030619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.
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Affiliation(s)
- Citlali Rodríguez-Gómez
- Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico; (C.R.-G.); (R.M.O.-R.)
| | - Lorena María Durán-Riveroll
- CONACYT—Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Tijuana-Ensenada 3918, Ensenada 22860, Baja California, Mexico
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar-und Meeresforschung, 27570 Bremerhaven, Germany
| | - Yuri B. Okolodkov
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Mar Mediterráneo 314, Fracc. Costa Verde, Boca del Río 94294, Veracruz, Mexico;
| | - Rosa María Oliart-Ros
- Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Veracruz, Veracruz 91897, Mexico; (C.R.-G.); (R.M.O.-R.)
| | | | - Allan D. Cembella
- Alfred-Wegener-Institut, Helmholtz Zentrum für Polar-und Meeresforschung, 27570 Bremerhaven, Germany
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21
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Li M, Zhang L, Zhang Q, Zi X, Lv R, Tang J, Zhou H. Impacts of Citric Acid and Malic Acid on Fermentation Quality and Bacterial Community of Cassava Foliage Silage. Front Microbiol 2020; 11:595622. [PMID: 33424799 PMCID: PMC7793898 DOI: 10.3389/fmicb.2020.595622] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
The microbiota and fermentation quality of cassava foliage (CF) ensiled in the absence of additive (CK), or the presence of citric acid (CA), malic acid (MA), and their combination with a Lactobacillus plantarum strain (CAL and MAL)were investigated. These additives reduced (P < 0.05) the pH, butyric acid, and ammonia-N contents but increased (P < 0.05) the lactic acid content, and CAL and MAL showed similar remarkable effects. Paenibacillus (mean, 27.81%) and Bacillus (mean, 16.04%) were the predominant strains in CF silage. The addition of CA or MAL increased the abundance of Paenibacillus (25.81–52.28% and 47.97%, respectively), and the addition of MA increased the abundance of Bacillus (15.76–32.48%) compared with the CK group. Moreover, CAL and MAL increased the abundances of the potentially desirable bacteria Cellulosimicrobium (CAL 0–12.73%), Hyphomicrobium (0–7.90% and 8.94%), and Oceanobacillus (0–8.37% and 3.08%) compared with the CK group. These findings suggested that CA and MA could enhance the silage quality of CF, and their combinations with Lactobacillus plantarum were more effective.
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Affiliation(s)
- Mao Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China.,Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, College of Tropical Crops, Hainan University, Danzhou, China
| | - Lidong Zhang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, College of Tropical Crops, Hainan University, Danzhou, China
| | - Qing Zhang
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangdong Research and Development Centre of Modern Agriculture (Woody Forage) Industrial Technology, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Integrative Microbiology Research Centre, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xuejuan Zi
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, Key Laboratory of Germplasm Resources of Tropical Special Ornamental Plants of Hainan Province, College of Forestry, College of Tropical Crops, Hainan University, Danzhou, China
| | - Renlong Lv
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Jun Tang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Hanlin Zhou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
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22
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Li J, Zhang B, Liu G, Liu Y, Yang H, Yang R, Huang Y, Li S, Chen T, Zhang W, Zhang G. Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:6338-6347. [PMID: 33118923 DOI: 10.1099/ijsem.0.004536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, endospore-forming and UV-resistant bacterial strain, designated strain TKL69T, was isolated from sandy soil sampled in the Taklimakan Desert. The strain grew at 20-50 °C, pH 6-9 and with 0-12 % (w/v) NaCl. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The only respiratory quinone was MK-7. The cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidyl glycerol, two unidentified aminophospholipids and one unidentified phospholipid were identified as the major polar lipids. Genomic DNA analysis revealed a G+C content of 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TKL69T has the highest similarity to Salinibacillus xinjiangensis CGMCC 1.12331T (96.9 %) but belongs to an independent taxon separated from other genera of the family Bacillaceae. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain TKL69T represents a novel species of a new genus, for which the name Radiobacillus gen. nov., sp. nov. is proposed, with the type strain being Radiobacillus deserti TKL69T (=JCM 33497T=CICC 24779T).
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Affiliation(s)
- Juan Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Yang Liu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploition and Application, Gansu Province, Lanzhou 730000, PR China
| | - Ruiqi Yang
- School of Geography and Environmental Engineering, Lanzhou City University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yixuan Huang
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Shiweng Li
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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23
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Zhu W, Li J, Wang X, Yang J, Lu S, Lai XH, Jin D, Huang Y, Zhang S, Pu J, Zhou J, Ren Z, Huang Y, Wu X, Xu J. Actinomyces wuliandei sp. nov., Corynebacterium liangguodongii sp. nov., Corynebacterium yudongzhengii sp. nov. and Oceanobacillus zhaokaii sp. nov., isolated from faeces of Tibetan antelope in the Qinghai-Tibet plateau of China. Int J Syst Evol Microbiol 2020; 70:3763-3774. [PMID: 32496179 DOI: 10.1099/ijsem.0.004232] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight Gram-stain-positive, rod-shaped bacterial strains were isolated from faeces of Tibetan antelopes on the Tibet-Qinghai Plateau of China. Genomic sequence analysis showed that the strains belong to the genera Actinomyces (strains 299T and 340), Corynebacterium (strains 2184T, 2185, 2183T and 2189) and Oceanobacillus (strains 160T and 143), respectively, with a percentage of similarity for the 16S rRNA gene under the species threshold of 98.7 % except for strains 160T and 143 with Oceanobacillus arenosus CAU 1183T (98.8 %). The genome sizes (and genomic G+C contents) were 3.1 Mb (49.4 %), 2.5 Mb (64.9 %), 2.4 Mb (66.1 %) and 4.1 Mb (37.1 %) for the type strains 299T, 2183T, 2184T and 160T, respectively. Two sets of the overall genome relatedness index values between our isolates and their corresponding closely related species were under species thresholds (95 % for average nucleotide identity, and 70 % for digital DNA-DNA hybridization). These results, together with deeper genotypic, genomic, phenotypic and biochemical analyses, indicate that these eight isolates should be classified as representing four novel species. Strain 299T (=CGMCC 1.16320T=JCM 33611T) is proposed as representing Actinomyces wuliandei sp. nov.; strain 2184T (=CGMCC 1.16417T=DSM 106203T) is proposed as representing Corynebacterium liangguodongii sp. nov.; strain 2183T (=CGMCC 1.16416T=DSM 106264T) is proposed as representing Corynebacterium yudongzhengii sp. nov.; and strain 160T (=CGMCC 1.16367T=DSM 106186T) is proposed as representing Oceanobacillus zhaokaii sp. nov.
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Affiliation(s)
- Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Junqin Li
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xiaoxia Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Juan Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Zhihong Ren
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China
| | - Xiaomin Wu
- Shaanxi Institute of Zoology, Xi'an 710032, PR China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China.,Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
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24
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Zhu WY, Yang L, Shi YJ, Mu CG, Wang Y, Kou YR, Yin M, Tang SK. Oceanobacillus halotolerans sp. nov., a bacterium isolated from salt lake in Xinjiang province, north-west China. Arch Microbiol 2020; 202:1545-1549. [PMID: 32246163 DOI: 10.1007/s00203-020-01865-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 11/26/2022]
Abstract
A bacterial strain, designated YIM 98839T, was isolated from the hypersaline sediment of Aiding Lake in Xinjiang province, North-West China. The strain was Gram-stain-positive, motile, aerobic, produced oval subterminal or central endospores in swollen sporangia. The whole-cell hydrolysates contain meso-diaminopimelic acid as the diagnostic cell-wall diamino acid. Galactose, fucose and ribose are the major whole-cell sugars. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and one unknown phospholipid. The predominant menaquinone is MK-7. The major fatty acids are anteiso-C15:0, anteiso-C17:0 and iso-C15:0. The DNA G + C content of the type strain is 37.0 mol%. Phylogenetic analysis indicated that the isolate belongs to the genus Oceanobacillus. However, it differed from its closest relative, Oceanobacillus limi H9BT in many physiological characteristics. Moreover, the DNA-DNA relatedness values between the novel isolate and the relative type strain was 20.2%. Based on comparative analysis of polyphasic taxonomic data, strain YIM 98839T represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus halotolerans sp. nov. is proposed. The type strain is YIM 98839T (= CGMCC 1.17002T = KCTC 43140T).
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Affiliation(s)
- Wen-Yong Zhu
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
- Yunnan Key Laboratory of Vaccine Research and Development On Severe Infections Diseases, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 650118, Kunming, PR China
| | - Li Yang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Yong-Jiang Shi
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Chang-Gai Mu
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China
| | - Yun Wang
- Life Science and Technology School, Lingnan Normal University, 524048, Zhanjiang, PR China
| | - Ya-Rong Kou
- Walvax Biotechnology Co., Ltd, 650106, Kunming, PR China
| | - Min Yin
- School of Medicine, Yunnan University, 650091, Kunming, PR China.
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, 650091, PR China.
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25
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Yu L, Tang X, Wei S, Qiu Y, Xu X, Xu G, Wang Q, Yang Q. Two novel species of the family Bacillaceae: Oceanobacillus piezotolerans sp. nov. and Bacillus piezotolerans sp. nov., from deep-sea sediment samples of Yap Trench. Int J Syst Evol Microbiol 2019; 69:3022-3030. [DOI: 10.1099/ijsem.0.003559] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Libo Yu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, PR China
| | - Xixiang Tang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Shiping Wei
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
| | - Yinkun Qiu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, PR China
| | - Xiashutong Xu
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Guangxin Xu
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
| | - Qilin Wang
- School of Ocean Sciences, China university of Geosciences (Beijing), Beijing, 100083, PR China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, PR China
| | - Qian Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, PR China
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26
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Azua-Bustos A, González-Silva C, Fernández-Martínez MÁ, Arenas-Fajardo C, Fonseca R, Martín-Torres FJ, Fernández-Sampedro M, Fairén AG, Zorzano MP. Aeolian transport of viable microbial life across the Atacama Desert, Chile: Implications for Mars. Sci Rep 2019; 9:11024. [PMID: 31439858 PMCID: PMC6706390 DOI: 10.1038/s41598-019-47394-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/16/2019] [Indexed: 11/19/2022] Open
Abstract
Here we inspect whether microbial life may disperse using dust transported by wind in the Atacama Desert in northern Chile, a well-known Mars analog model. By setting a simple experiment across the hyperarid core of the Atacama we found that a number of viable bacteria and fungi are in fact able to traverse the driest and most UV irradiated desert on Earth unscathed using wind-transported dust, particularly in the later afternoon hours. This finding suggests that microbial life on Mars, extant or past, may have similarly benefited from aeolian transport to move across the planet and find suitable habitats to thrive and evolve.
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Affiliation(s)
- Armando Azua-Bustos
- Centro de Astrobiología (CSIC-INTA), 28850, Madrid, Spain.
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile.
| | | | | | | | - Ricardo Fonseca
- Division of Space Technology, Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden
| | - F Javier Martín-Torres
- Division of Space Technology, Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden
- Instituto Andaluz de Ciencias de la Tierra (UGR-CSIC), Armilla, Granada, Spain
| | | | - Alberto G Fairén
- Centro de Astrobiología (CSIC-INTA), 28850, Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca, 14853, NY, USA
| | - María-Paz Zorzano
- Centro de Astrobiología (CSIC-INTA), 28850, Madrid, Spain
- Division of Space Technology, Department of Computer Science, Electrical and Space Engineering, Luleå University of Technology, Luleå, Sweden
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27
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Merino N, Aronson HS, Bojanova DP, Feyhl-Buska J, Wong ML, Zhang S, Giovannelli D. Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context. Front Microbiol 2019; 10:780. [PMID: 31037068 PMCID: PMC6476344 DOI: 10.3389/fmicb.2019.00780] [Citation(s) in RCA: 218] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/27/2019] [Indexed: 01/21/2023] Open
Abstract
Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.
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Affiliation(s)
- Nancy Merino
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, United States
| | - Heidi S Aronson
- Department of Biology, University of Southern California, Los Angeles, CA, United States
| | - Diana P Bojanova
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Michael L Wong
- Department of Astronomy - Astrobiology Program, University of Washington, Seattle, WA, United States.,NASA Astrobiology Institute's Virtual Planetary Laboratory, University of Washington, Seattle, WA, United States
| | - Shu Zhang
- Section of Infection and Immunity, Herman Ostrow School of Dentistry of USC, University of Southern California, Los Angeles, CA, United States
| | - Donato Giovannelli
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Biology, University of Naples "Federico II", Naples, Italy.,Department of Marine and Coastal Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States.,Institute for Biological Resources and Marine Biotechnology, National Research Council of Italy, Ancona, Italy
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28
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Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish. Food Microbiol 2019; 82:560-572. [PMID: 31027819 DOI: 10.1016/j.fm.2019.03.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/10/2023]
Abstract
Hákarl is produced by curing of the Greenland shark (Somniosus microcephalus) flesh, which before fermentation is toxic due to the high content of trimethylamine (TMA) or trimethylamine N-oxide (TMAO). Despite its long history of consumption, little knowledge is available on the microbial consortia involved in the fermentation of this fish. In the present study, a polyphasic approach based on both culturing and DNA-based techniques was adopted to gain insight into the microbial species present in ready-to-eat hákarl. To this aim, samples of ready-to-eat hákarl were subjected to viable counting on different selective growth media. The DNA directly extracted from the samples was further subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S amplicon-based sequencing. Moreover, the presence of Shiga toxin-producing Escherichia coli (STEC) and Pseudomonas aeruginosa was assessed via qualitative real-time PCR assays. pH values measured in the analyzed samples ranged from between 8.07 ± 0.06 and 8.76 ± 0.00. Viable counts revealed the presence of total mesophilic aerobes, lactic acid bacteria and Pseudomonadaceae. Regarding bacteria, PCR-DGGE analysis highlighted the dominance of close relatives of Tissierella creatinophila. For amplicon sequencing, the main operational taxonomic units (OTUs) shared among the data set were Tissierella, Pseudomonas, Oceanobacillus, Abyssivirga and Lactococcus. The presence of Pseudomonas in the analyzed samples supports the hypothesis of a possible role of this microorganism on the detoxification of shark meat from TMAO or TMA during fermentation. Several minor OTUs (<1%) were also detected, including Alkalibacterium, Staphylococcus, Proteiniclasticum, Acinetobacter, Erysipelothrix, Anaerobacillus, Ochrobactrum, Listeria and Photobacterium. Analysis of the yeast and filamentous fungi community composition by PCR-DGGE revealed the presence of close relatives of Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida zeylanoides, Saccharomyces cerevisiae, Debaryomyces, Torulaspora, Yamadazyma, Sporobolomyces, Alternaria, Cladosporium tenuissimum, Moristroma quercinum and Phoma/Epicoccum, and some of these species probably play key roles in the development of the sensory qualities of the end product. Finally, qualitative real-time PCR assays revealed the absence of STEC and Pseudomonas aeruginosa in all of the analyzed samples.
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Kevbrin VV. Isolation and Cultivation of Alkaliphiles. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 172:53-84. [DOI: 10.1007/10_2018_84] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, Sokhna C, Raoult D, Lagier JC. Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese. Antonie van Leeuwenhoek 2018; 112:785-796. [DOI: 10.1007/s10482-018-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
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Wang D, Xiang Y, Jiang C, Zhang J, Hua Z, Niu L, Luo L. Pueribacillus theae gen. nov., sp. nov., isolated from Pu'er tea. Int J Syst Evol Microbiol 2018; 68:2878-2882. [PMID: 30028280 DOI: 10.1099/ijsem.0.002913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
A novel bacterial strain, designated T8T, isolated from ripened Pu'er tea, was investigated by using a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, sporogenous and rod-shaped with flagella. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Bacillaceae in the class Bacilli and represented an independent taxon separated from other genera. Strain T8T shared low levels of 16S rRNA gene sequence similarity (<94 %) to members of other genera in the family Bacillaceae and was most closely related to Bacillus composti SgZ-9T (93.3 % sequence similarity). The DNA G+C content of strain T8T was 40 mol%. The major fatty acids (>10 %) of strain T8T were iso-C15 : 0 and iso-C16 : 0. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. MK-7 (62 %), MK-6 (31 %) and MK-8 (7 %) were detected as the isoprenoid quinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine and six unidentified phospholipids. On the basis of the polyphasic evidence presented, strain T8T is considered to represent a novel genus and species in the family Bacillaceae, for which we propose the name Pueribacillus theae gen. nov., sp. nov. The type strain is T8T (=CGMCC 1.15924T=KCTC 333888T).
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Affiliation(s)
- Dejia Wang
- 1Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PR China.,2College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yangquan Xiang
- 1Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Chengyan Jiang
- 1Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Juan Zhang
- 1Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Ziyi Hua
- 3Experimental Center for Life Sciences, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Lili Niu
- 1Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PR China
| | - Liqiang Luo
- 2College of Sciences, Shanghai University, Shanghai 200444, PR China
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Zapata-Pérez R, Gil-Ortiz F, Martínez-Moñino AB, García-Saura AG, Juanhuix J, Sánchez-Ferrer Á. Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis. Open Biol 2018; 7:rsob.160327. [PMID: 28446708 PMCID: PMC5413906 DOI: 10.1098/rsob.160327] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/30/2017] [Indexed: 01/08/2023] Open
Abstract
Macrodomains are ubiquitous conserved domains that bind or transform ADP-ribose (ADPr) metabolites. In humans, they are involved in transcription, X-chromosome inactivation, neurodegeneration and modulating PARP1 signalling, making them potential targets for therapeutic agents. Unfortunately, some aspects related to the substrate binding and catalysis of MacroD-like macrodomains still remain unclear, since mutation of the proposed catalytic aspartate does not completely abolish enzyme activity. Here, we present a functional and structural characterization of a macrodomain from the extremely halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiMacroD), related to hMacroD1/hMacroD2, shedding light on substrate binding and catalysis. The crystal structures of D40A, N30A and G37V mutants, and those with MES, ADPr and ADP bound, allowed us to identify five fixed water molecules that play a significant role in substrate binding. Closure of the β6–α4 loop is revealed as essential not only for pyrophosphate recognition, but also for distal ribose orientation. In addition, a novel structural role for residue D40 is identified. Furthermore, it is revealed that OiMacroD not only catalyses the hydrolysis of O-acetyl-ADP-ribose but also reverses protein mono-ADP-ribosylation. Finally, mutant G37V supports the participation of a substrate-coordinated water molecule in catalysis that helps to select the proper substrate conformation.
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Affiliation(s)
- Rubén Zapata-Pérez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | | | - Ana Belén Martínez-Moñino
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Antonio Ginés García-Saura
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus Espinardo, 30100 Murcia, Spain
| | - Jordi Juanhuix
- CELLS-ALBA Synchrotron Light Source, 08290 Barcelona, Spain
| | - Álvaro Sánchez-Ferrer
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, Regional Campus of International Excellence 'Campus Mare Nostrum', University of Murcia, Campus Espinardo, 30100 Murcia, Spain .,Murcia Biomedical Research Institute (IMIB-Arrixaca), 30120 Murcia, Spain
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Zaikova E, Benison KC, Mormile MR, Johnson SS. Microbial communities and their predicted metabolic functions in a desiccating acid salt lake. Extremophiles 2018; 22:367-379. [PMID: 29350297 DOI: 10.1007/s00792-018-1000-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/02/2018] [Indexed: 11/30/2022]
Abstract
The waters of Lake Magic in Western Australia are among the most geochemically extreme on Earth. This ephemeral saline lake is characterized by pH as low as 1.6 salinity as high as 32% total dissolved solids, and unusually complex geochemistry, including extremely high concentrations of aluminum, silica, and iron. We examined the microbial composition and putative function in this extreme acid brine environment by analyzing lake water, groundwater, and sediment samples collected during the austral summer near peak evapoconcentration. Our results reveal that the lake water metagenome, surprisingly, was comprised of mostly eukaryote sequences, particularly fungi and to a lesser extent, green algae. Groundwater and sediment samples were dominated by acidophilic Firmicutes, with eukaryotic community members only detected at low abundances. The lake water bacterial community was less diverse than that in groundwater and sediment, and was overwhelmingly represented by a single OTU affiliated with Salinisphaera. Pathways associated with halotolerance were found in the metagenomes, as were genes associated with biosynthesis of protective carotenoids. During periods of complete desiccation of the lake, we hypothesize that dormancy and entrapment in fluid inclusions in halite crystals may increase long-term survival, leading to the resilience of complex eukaryotes in this extreme environment.
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Affiliation(s)
- Elena Zaikova
- Department of Biology, Georgetown University, Washington, USA
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, USA
| | - Melanie R Mormile
- Department of Biology, Missouri University of Science and Technology, Rolla, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, USA. .,Program on Science, Technology, and International Affairs, Georgetown University, Washington, USA.
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Aidingibacillus halophilus gen. nov., sp. nov., a novel member of the family Bacillaceae. Antonie van Leeuwenhoek 2017; 111:601-608. [PMID: 29134392 DOI: 10.1007/s10482-017-0980-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/04/2017] [Indexed: 10/18/2022]
Abstract
A Gram-positive, non-motile, asporogenous and aerobic bacterium, designated YIM 98012T, was isolated from a salt lake in China. Strain YIM 98012T was found to be catalase and oxidase positive. Optimal growth of strain YIM 98012T was observed at 37 °C and pH 7.0 and it was found to grow in the presence of 5-20% (w/v) NaCl (optimum 10% NaCl). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel strain is affiliated with the family Bacillaceae of the phylum Firmicutes and that it shares high (94.7%) sequence similarity with Alteribacillus persepolensis DSM 21632T and does not show sequence similarities of more than 94.0% to known members of other related genera. The major fatty acids (> 10%) were identified as anteiso-C15:0, anteiso-C17:0, iso-C16:0 and C16:0. The genomic DNA G+C content was determined to be 41.0 mol% and the dominated respiratory quinone was identified as MK-7. The cell wall peptidoglycan of strain YIM 98012T was found to contain meso-diaminopimelic acid, while the polar lipids profile was found to include diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Based on physiological and chemotaxonomic characteristics, strain YIM 98012T is concluded to be the type strain of the type species of a novel genus in the family Bacillaceae for which the name Aidingibacillus halophilus gen. nov., sp. nov. is proposed. The type strain is YIM 98012T (= KCTC 33868T = DSM 104332T).
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Guo LY, Wang NN, Wang XQ, Chen GJ, Du ZJ. Lentibacillus sediminis sp. nov., isolated from a marine saltern. Int J Syst Evol Microbiol 2017; 67:3946-3950. [DOI: 10.1099/ijsem.0.002228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ling-Yun Guo
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Nan-Nan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Xiao-Qun Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
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Bhatt HB, Azmatunnisa Begum M, Chintalapati S, Chintalapati VR, Singh SP. Desertibacillus haloalkaliphilus gen. nov., sp. nov., isolated from a saline desert. Int J Syst Evol Microbiol 2017; 67:4435-4442. [PMID: 28920841 DOI: 10.1099/ijsem.0.002310] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, rod-shaped and endospore-forming bacteria that represent a single species, designated strains KJ1-10-99T and KJ1-10-93, were isolated from a saline desert of Little Rann of Kutch, Gujarat, India. Analysis of 16S rRNA gene sequences revealed that the isolates belonged to the family Bacillaceae and were closely related to each other with 16S rRNA gene sequence similarity of 99.9 %. However, these two isolates formed a novel phylogenetic branch within this family. Both strains were aerobic, catalase and oxidase positive, and could grow optimally at 37 °C and pH 9. Further, strains KJ1-10-99T and KJ1-10-93 grew optimally at a NaCl concentration of 7.5 and 15 % (w/v), respectively. Both strains shared highest sequence similarity with Fermentibacillus polygoni IEB3T (96.90 %) followed by Bacillus nanhaiisediminis NH3T (96.3 %) and Bacillus alkalinitrilicus ANL-iso4T (96.3 %). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17:0, C16 : 0, and iso-C15 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol in both strains. The predominant isoprenoid quinone was MK-7 in both the strains. The peptidoglycan contained meso-diaminopimelic acid (meso-DAP) as the diagnostic diamino acid. The DNA G+C content of strains KJ1-10-99T and KJ1-10-93 were 48.7 and 48.9 mol% respectively. Both strains could be distinguished from closest phylogenetic neighbours based on a number of phenotypic properties. On the basis of polyphasic taxonomic analysis and phylogenetic data, we conclude that the strains KJ1-10-99T (=LMG 29918T=KCTC 33878T) and KJ1-10-93 (=LMG 29919=KCTC 33877) represent a novel species of a new genus in the family Bacillaceae, order Bacillales, for which the name Desertibacillus haloalkaliphilus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Hitarth B Bhatt
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot-360005, Gujarat, India
| | - M Azmatunnisa Begum
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500085, India
| | - Sasikala Chintalapati
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad 500085, India
| | - Venkata Ramana Chintalapati
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot-360005, Gujarat, India
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Khelaifia S, Lagier JC, Bibi F, Azhar EI, Croce O, Padmanabhan R, Jiman-Fatani AA, Yasir M, Robert C, Andrieu C, Fournier PE, Raoult D. Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:248-58. [PMID: 27093109 DOI: 10.1089/omi.2016.0004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.
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Affiliation(s)
- Saber Khelaifia
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Jean-Christophe Lagier
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Fehmida Bibi
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .,3 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Olivier Croce
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Roshan Padmanabhan
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Asif Ahmad Jiman-Fatani
- 4 Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Muhammad Yasir
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Catherine Robert
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Claudia Andrieu
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Pierre-Edouard Fournier
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Didier Raoult
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.,2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
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Amoozegar MA, Bagheri M, Makhdoumi A, Mehrshad M, Didari M, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Oceanobacillus longus sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int J Syst Evol Microbiol 2016; 66:4225-4230. [DOI: 10.1099/ijsem.0.001339] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mohammad Ali Amoozegar
- Department of Microbiology, Extremophiles Laboratory, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Bagheri
- Department of Microbiology, Extremophiles Laboratory, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), ACECR, Tehran, Iran
| | - Ali Makhdoumi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maliheh Mehrshad
- Department of Microbiology, Extremophiles Laboratory, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Maryam Didari
- Department of Microbiology, Extremophiles Laboratory, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
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Draft Genome Sequence of an Oceanobacillus sp. Strain Isolated from Soil in a Burial Crypt. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00701-16. [PMID: 27469952 PMCID: PMC4966456 DOI: 10.1128/genomea.00701-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We present the draft genome of an Oceanobacillus sp. strain isolated from spores found in soil samples from a burial crypt of the Cathedral of Sant'Antonio Abate in Castelsardo, Italy. The data obtained indicated the closest relation of the strain with Oceanobacillus caeni.
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Laport MS, Pontes PVM, Dos Santos DS, Santos-Gandelman JDF, Muricy G, Bauwens M, Giambiagi-deMarval M, George I. Antibiotic resistance genes detected in the marine sponge Petromica citrina from Brazilian coast. Braz J Microbiol 2016; 47:617-20. [PMID: 27287338 PMCID: PMC4927650 DOI: 10.1016/j.bjm.2016.04.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/11/2016] [Indexed: 01/27/2023] Open
Abstract
Although antibiotic-resistant pathogens pose a significant threat to human health, the environmental reservoirs of the resistance determinants are still poorly understood. This study reports the detection of resistance genes (ermB, mecA, mupA, qnrA, qnrB and tetL) to antibiotics among certain culturable and unculturable bacteria associated with the marine sponge Petromica citrina. The antimicrobial activities elicited by P. citrina and its associated bacteria are also described. The results indicate that the marine environment could play an important role in the development of antibiotic resistance and the dissemination of resistance genes among bacteria.
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Affiliation(s)
- Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil; Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.
| | - Paula Veronesi Marinho Pontes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Daniela Silva Dos Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Juliana de Fátima Santos-Gandelman
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Guilherme Muricy
- Museu Nacional, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Mathieu Bauwens
- Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Marcia Giambiagi-deMarval
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Isabelle George
- Département de Biologie des Organismes, Laboratoire de Biologie Marine, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
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Yang LL, Tang SK, Chu X, Jiang Z, Xu LH, Zhi XY. Oceanobacillus endoradicis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis. Antonie van Leeuwenhoek 2016; 109:957-64. [PMID: 27059624 DOI: 10.1007/s10482-016-0695-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/02/2016] [Indexed: 11/28/2022]
Abstract
A bacterial strain, py1294(T), isolated from a root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, southwest China, was characterised by using a polyphasic approach to clarify its taxonomic position. Strain py1294(T) was found to be Gram-positive, aerobic, spore-forming, peritrichous flagella and rod shaped. Growth was found to occur in the presence of 0-8 % (w/v) NaCl (optimum 1-3 %), at pH 6.5-9.5 (optimum 8.0) and at 10-42 °C (optimum 30 °C). The major cellular fatty acids were identified as anteiso-C15:0, anteiso-C17:0, iso-C16:0 and iso-C14:0. The predominant quinone was identified as MK-7 and a minor amount of MK-6 was detected. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The cell wall peptidoglycan was found to contain meso-diaminopimelic acid. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain py1294(T) forms a well-supported clade with Oceanobacillus damuensis PT-20(T) (97.9 % sequence similarity) within the genus Oceanobacillus, although it also shares a high sequence similarity with Ornithinibacillus contaminans (97.5 %). Crucially, the DNA-DNA relatedness value between strain py1294(T) and O. damuensis PT-20(T) was 29.7 ± 3.2 %. The G+C content was determined to be 42.3 mol%. On the basis of the phylogenetic and phenotypic data, a novel species Oceanobacillus endoradicis sp. nov. is proposed, with py1294(T) (=DSM 100726(T) = KCTC 33731(T)) as the type strain.
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Affiliation(s)
- Ling-Ling Yang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Shu-Kun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiao Chu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Zhao Jiang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Li-Hua Xu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China.
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Abstract
Members of the family Bacillaceae are among the most robust bacteria on Earth, which is mainly due to their ability to form resistant endospores. This trait is believed to be the key factor determining the ecology of these bacteria. However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and growth stimulation (e.g., via suppression of plant pathogens and phosphate solubilization). In this review, we describe the high functional and genetic diversity that is found within the Bacillaceae (a family of low-G+C% Gram-positive spore-forming bacteria), their roles in ecology and in applied sciences related to agriculture. We then pose questions with respect to their ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some members of Bacillaceae. Such social behavior, which includes cell-to-cell signaling via quorum sensing or other mechanisms (e.g., the production of extracellular hydrolytic enzymes, toxins, antibiotics and/or surfactants) is a key determinant of their lifestyle and is also believed to drive diversification processes. It is only with a deeper understanding of cell-to-cell interactions that we will be able to understand the ecological and diversification processes of natural populations within the family Bacillaceae. Ultimately, the resulting improvements in understanding will benefit practical efforts to apply representatives of these bacteria in promoting plant growth as well as biological control of plant pathogens.
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Amoozegar MA, Bagheri M, Makhdoumi A, Nikou MM, Fazeli SAS, Schumann P, Spröer C, Sánchez-Porro C, Ventosa A. Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2016; 66:1317-1322. [DOI: 10.1099/ijsem.0.000952] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, Faculty of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran,Tehran,Iran
| | - Maryam Bagheri
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC),ACECR, Tehran,Iran
| | - Ali Makhdoumi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad,Mashhad,Iran
| | | | | | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures,Inhoffenstraße 7B, 38124 Braunschweig,Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures,Inhoffenstraße 7B, 38124 Braunschweig,Germany
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla,41012 Sevilla,Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla,41012 Sevilla,Spain
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Guerreiro I, Serra CR, Enes P, Couto A, Salvador A, Costas B, Oliva-Teles A. Effect of short chain fructooligosaccharides (scFOS) on immunological status and gut microbiota of gilthead sea bream (Sparus aurata) reared at two temperatures. FISH & SHELLFISH IMMUNOLOGY 2016; 49:122-31. [PMID: 26721230 DOI: 10.1016/j.fsi.2015.12.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/16/2015] [Accepted: 12/18/2015] [Indexed: 05/27/2023]
Abstract
The effects of dietary short chain fructooligosaccharides (scFOS) incorporation on hematology, fish immune status, gut microbiota composition, digestive enzymes activities, and gut morphology, was evaluated in gilthead sea bream (Sparus aurata) juveniles reared at 18 °C and 25 °C. For that purpose, fish with 32 g were fed diets including 0, 0.1, 0.25 and 0.5% scFOS during 8 weeks. Overall, scFOS had only minor effects on gilthead sea bream immune status. Lymphocytes decreased in fish fed the 0.1% scFOS diet. Fish fed the 0.5% scFOS diet presented increased nitric oxide (NO) production, while total immunoglobulins (Ig) dropped in those fish, but only in the ones reared at 25 °C. Red blood cells, hemoglobin, bactericidal activity and NO were higher at 25 °C, whereas total white blood cells, circulating thrombocytes, monocytes and neutrophils were higher at 18 °C. In fish fed scFOS, lymphocytes were higher at 18 °C. Total Ig were also higher at 18 °C but only in fish fed 0.1% and 0.5% scFOS diets. No differences in gut bacterial profiles were detected by PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) between dietary treatments. However, group's similarity was higher at 25 °C. Digestive enzymes activities were higher at 25 °C but were unaffected by prebiotics incorporation. Gut morphology was also unaffected by dietary prebiotic incorporation. Overall, gut microbiota composition, digestive enzymes activities and immunity parameters were affected by rearing temperature whereas dietary scFOS incorporation had only minor effects on these parameters. In conclusion, at the tested levels scFOS does not seem worthy of including it in gilthead sea bream juveniles diets.
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Affiliation(s)
- Inês Guerreiro
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007 Porto, Portugal.
| | - Cláudia R Serra
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Paula Enes
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Ana Couto
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Andreia Salvador
- CEB - Centro de Engenharia Biológica, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Benjamín Costas
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Aires Oliva-Teles
- CIMAR/CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, Ed. FC4, 4169-007 Porto, Portugal
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Liu Y, Liang J, Zhang Z, Yu M, Wang M, Zhang XH. Aureibacillus halotolerans gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2015; 65:3950-3958. [PMID: 28875917 DOI: 10.1099/ijsem.0.000518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, strictly aerobic, spore-forming and rod-shaped motile bacterium with peritrichous flagellae, designated strain S1203T, was isolated from the sediment of the northern Okinawa Trough. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S1203T formed a lineage within the family Bacillaceae that was distinct from the most closely related genera Bacillus, Bhargavaea, Planomicrobium and Virgibacillus with gene sequence similarities ranging from 86.2 to 93.76 %. Optimal growth occurred in the presence of 4-8 % (w/v) NaCl, at pH 7.0-8.0 and 25-32 °C. The cell-wall peptidoglycan was based on meso-diaminopimelic acid and unsaturated menaquinone with seven isoprene units (MK-7) as the predominant respiratory quinone. The major fatty acids (>10 % of total fatty acids) were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0.The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and an unidentified phospholipid. The DNA G+C content of strain S1203T was 47.7 mol%. On the basis of polyphasic analysis, strainS1203T was considered to represent a novel species in a new genus of the family Bacillaceae, for which the name Aureibacillus halotolerans gen. nov., sp. nov. is proposed; the type strain of Aureibacillus halotolerans is S1203T ( = DSM 28697T = JCM 30067T = MCCC 1K00259T).
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Affiliation(s)
- Yan Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Jing Liang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Zenghu Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Min Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
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47
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Lagier JC, Khelaifia S, Azhar EI, Croce O, Bibi F, Jiman-Fatani AA, Yasir M, Helaby HB, Robert C, Fournier PE, Raoult D. Genome sequence of Oceanobacillus picturae strain S1, an halophilic bacterium first isolated in human gut. Stand Genomic Sci 2015; 10:91. [PMID: 26523201 PMCID: PMC4627390 DOI: 10.1186/s40793-015-0081-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Oceanobacillus picturae is a strain of a moderately halophilic bacterium, first isolated from a mural painting. We demonstrate, for the first time, the culture of human Oceanobacillus picturae, strain S1(T), whose genome is described here, from a stool sample collected from a 25-year-old Saoudian healthy individual. We used a slightly modified standard culture medium adding 100 g/L of NaCl. We provide a short description of this strain including its MALDI-TOF spectrum, the main identification tool currently used in clinical microbiology. The 3,675,175 bp long genome exhibits a G + C content of 39.15 % and contains 3666 protein-coding and 157 RNA genes. The draft genome sequence of Oceanobacillus picturae has a similar size to the Oceanobacillus kimchii (respectively 3.67 Mb versus 3.83 Mb). The G + C content was higher compared with Oceanobacillus kimchii (respectively 39.15 % and 35.2 %). Oceanobacillus picturae shared almost identical number of genes (3823 genes versus 3879 genes), with a similar ratio of genes per Mb (1041 genes/Mb versus 1012 genes/Mb). The genome sequencing of Oceanobacillus picturae strain S1 isolated for the first time in a human, will be added to the 778 genome projects from the gastrointestinal tract listed by the international consortium Human Microbiome Project.
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Affiliation(s)
- Jean-Christophe Lagier
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Saber Khelaifia
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Esam Ibraheem Azhar
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Olivier Croce
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Fehmida Bibi
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- />Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Huda Ben Helaby
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Pierre-Edouard Fournier
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
| | - Didier Raoult
- />Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, L’Institut de Recherche pour le Développement 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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48
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You YH, Park JM, Park JH, Kim JG. Specific rhizobacterial resources: characterization and comparative analysis from contrasting coastal environments of Korea. J Basic Microbiol 2015; 56:92-101. [PMID: 26367263 DOI: 10.1002/jobm.201500195] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/05/2015] [Indexed: 11/12/2022]
Abstract
This study analyzed the rhizobacterial distribution from two coasts, which show contrasting climates and geographical and geological characteristics, to secure specific microbial resources. Furthermore, rhizobacteria were characterized and the results were comparatively analyzed with reference to the characteristics of two coastal environments. For this purpose, three representative halophyte species communities native to the Dokdo Islands and the East Sea coast of Korea were selected. Partial identification of rhizobacteria showed a clear difference between each sampling site and halophyte. Furthermore, isolates were characterized by their growth properties under NaCl or pH gradients related with previous geographical, geological, and climatic studies of the Dokdo Islands and the East Sea coast. A high proportion of the East Sea isolates showed halotolerance, but a high proportion of Dokdo isolates shared halophilic traits. Meanwhile, a higher proportion of East Sea isolates grew at a wider range of pH values than those of the Dokdo Islands. The results of our study suggest that unique rhizobacterial resources developed under specific rhizospheric conditions derived from halophytes interacting with their specific environment, even within the same coastal halophytic species. Therefore, this study proposes the necessity of securing characterized and unique microbial resources to apply to specific environments for the purpose of recovering and restoring sand dunes or salt-damaged agricultural lands.
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Affiliation(s)
- Young-Hyun You
- School of Life Science, Kyungpook National University, Daegu, Republic of Korea.,Horticultural & Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jong Myong Park
- School of Life Science, Kyungpook National University, Daegu, Republic of Korea.,Distribution Safety Team, Safety Center, LOTTE R&D Center, Seoul, Republic of Korea
| | - Jong-Han Park
- Horticultural & Herbal Crop Environment Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jong-Guk Kim
- School of Life Science, Kyungpook National University, Daegu, Republic of Korea
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49
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Kim W, Siamphan C, Kim JH, Sukhoom A. Oceanobacillus arenosus sp. nov., a moderately halophilic bacterium isolated from marine sand. Int J Syst Evol Microbiol 2015; 65:2943-2948. [DOI: 10.1099/ijs.0.000360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterium, designated CAU 1183T, was isolated from marine sand and its taxonomic position was investigated by using a polyphasic approach. The bacterium grew optimally at 30 °C, at pH 8.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1183T formed a distinct lineage within the genus Oceanobacillus and exhibited the highest similarity to Oceanobacillus chungangensis CAU 1051T (97.6 %). The strain contained MK-7 as the predominant isoprenoid quinone and anteiso-C15 : 0 was the major cellular fatty acid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The polar lipid pattern of strain CAU 1183T consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified lipids, including two phospholipids, two glycolipids, a phosphoglycolipid and two lipids. The G+C content of the genomic DNA was 37.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain CAU 1183T should be assigned to a novel species in the genus Oceanobacillus, for which the name Oceanobacillus arenosus sp. nov. is proposed. The type strain is CAU 1183T ( = KCTC 33037T = CECT 8560T).
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Affiliation(s)
- Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Chatuphon Siamphan
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Ampaitip Sukhoom
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand
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50
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Abstract
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
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