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Pallen MJ. The dynamic history of prokaryotic phyla: discovery, diversity and division. Int J Syst Evol Microbiol 2024; 74. [PMID: 39250184 PMCID: PMC11382960 DOI: 10.1099/ijsem.0.006508] [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: 09/10/2024] Open
Abstract
Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.
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Affiliation(s)
- Mark J Pallen
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
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Jiao JY, Abdugheni R, Zhang DF, Ahmed I, Ali M, Chuvochina M, Dedysh SN, Dong X, Göker M, Hedlund BP, Hugenholtz P, Jangid K, Liu SJ, Moore ERB, Narsing Rao MP, Oren A, Rossello-Mora R, Rekadwad BN, Salam N, Shu W, Sutcliffe IC, Teo WFA, Trujillo ME, Venter SN, Whitman WB, Zhao G, Li WJ. Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era. Natl Sci Rev 2024; 11:nwae168. [PMID: 39071100 PMCID: PMC11275469 DOI: 10.1093/nsr/nwae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 07/30/2024] Open
Abstract
Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Rashidin Abdugheni
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
| | - Iftikhar Ahmed
- National Culture Collection of Pakistan (NCCP), Land Resources Research Institute (LRRI), National Agricultural Research Centre (NARC), Islamabad 45500, Pakistan
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig D-38124, Germany
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Queensland 4072, Australia
| | - Kamlesh Jangid
- Bioenergy Group, MACS Collection of Microorganisms, Agharkar Research Institute, Pune 411004, India
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Edward R B Moore
- Department of Infectious Disease, Institute for Biomedicine, and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40234, Sweden
| | - Manik Prabhu Narsing Rao
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería, Universidad Autónoma de Chile, Talca 3460000, Chile
| | - Aharon Oren
- The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles 070190, Spain
| | - Bhagwan Narayan Rekadwad
- MicrobeAI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Nimaichand Salam
- National Agri-Food Biotechnology Institute, Knowledge City, Mohali 140306, India
| | - Wensheng Shu
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Martha E Trujillo
- Microbiology and Genetics Department, University of Salamanca, Salamanca 37008, Spain
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0028, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Guoping Zhao
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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Marshall B, Amritkar K, Wolfe M, Kaçar B, Landick R. Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway. Front Microbiol 2023; 14:1286626. [PMID: 38029103 PMCID: PMC10663253 DOI: 10.3389/fmicb.2023.1286626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron-sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron-sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.
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Affiliation(s)
- Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Kaustubh Amritkar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Michael Wolfe
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
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Vishnoi V, Hoedt EC, Gould T, Carroll G, Carroll R, Lott N, Pockney P, Smith SR, Keely S. A pilot study: intraoperative 16S rRNA sequencing versus culture in predicting colorectal incisional surgical site infection. ANZ J Surg 2023; 93:2464-2472. [PMID: 37025037 DOI: 10.1111/ans.18455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Surgical Site Infection (SSI) of the abdominal incision is a dreaded complication following colorectal surgery. Identifying the intraoperative surgical site microbes may provide clarity in the pathogenesis of SSIs. Genomic sequencing has revolutionized the ability to identify microbes from clinical samples. Utilization of 16S rRNA amplicon sequencing to characterize the intraoperative surgical site may provide the critical information required to predict and prevent infection in colorectal surgery. METHODS This is a pilot, prospective observational study of 50 patients undergoing elective colorectal resection. At completion of surgery, prior to skin closure, swabs were taken from the subcutaneous tissue of the abdominal incision to investigate the microbial profile. Dual swabs were taken to compare standard culture technique and 16S rRNA sequencing to establish if a microbial profile was associated with postoperative SSI. RESULTS 8/50 patients developed an SSI, which was more likely in those undergoing open surgery (5/15 33.3% versus 3/35, 8.6%; P = 0.029). 16S rRNA amplicon sequencing was more sensitive in microbial detection compared to traditional culture. Both culture and 16S rRNA demonstrated contamination of the surgical site, predominantly with anaerobes. Culture was not statistically predictive of infection. 16S rRNA amplicon sequencing was not statistically predictive of infection, however, it demonstrated patients with an SSI had an increased biodiversity (not significant) and a greater relative abundance (not significant) of pathogens such as Bacteroidacaea and Enterobacteriaceae within the intraoperative site. CONCLUSIONS 16S rRNA amplicon sequencing has demonstrated a potential difference in the intraoperative microbial profile of those that develop an infection. These findings require validation through powered experiments to determine the overall clinical significance.
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Affiliation(s)
- Veral Vishnoi
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Emily C Hoedt
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Tiffany Gould
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Georgia Carroll
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Rosemary Carroll
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Natalie Lott
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Peter Pockney
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Stephen R Smith
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
- Department of Surgical Services, Calvary Mater Hospital, Newcastle, New South Wales, Australia
| | - Simon Keely
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
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Kestel JH, Field DL, Bateman PW, White NE, Allentoft ME, Hopkins AJM, Gibberd M, Nevill P. Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157556. [PMID: 35882340 DOI: 10.1016/j.scitotenv.2022.157556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.
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Affiliation(s)
- Joshua H Kestel
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia.
| | - David L Field
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Philip W Bateman
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Behavioural Ecology Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Anna J M Hopkins
- Molecular Ecology and Evolution Group (MEEG), School of Science, Edith Cowan University, Joondalup 6027, Australia
| | - Mark Gibberd
- Centre for Crop Disease Management (CCDM), School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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Zhang M, Hu Y, Liu J, Pei Y, Tang K, Lei Y. Biodeterioration of collagen-based cultural relics: A review. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2021.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Kalariya KA, Meena RP, Poojara L, Shahi D, Patel S. Characterization of squalene synthase gene from Gymnema sylvestre R. Br. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021. [DOI: 10.1186/s43088-020-00094-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant.
Results
Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br.
Conclusion
This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.
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Siqueira JF, Rôças IN. A critical analysis of research methods and experimental models to study the root canal microbiome. Int Endod J 2021; 55 Suppl 1:46-71. [PMID: 34714548 DOI: 10.1111/iej.13656] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.
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Affiliation(s)
- José F Siqueira
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
| | - Isabela N Rôças
- Department of Endodontics and Molecular Microbiology Laboratory, Faculty of Dentistry, Grande Rio University, Rio de Janeiro, Brazil.,Department of Dental Research, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
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Functional metagenomic analysis of quorum sensing signaling in a nitrifying community. NPJ Biofilms Microbiomes 2021; 7:79. [PMID: 34711833 PMCID: PMC8553950 DOI: 10.1038/s41522-021-00250-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/08/2021] [Indexed: 01/12/2023] Open
Abstract
Quorum sensing (QS) can function to shape the microbial community interactions, composition, and function. In wastewater treatment systems, acylated homoserine lactone (AHL)-based QS has been correlated with the conversion of floccular biomass into microbial granules, as well as EPS production and the nitrogen removal process. However, the role of QS in such complex communities is still not fully understood, including the QS-proficient taxa and the functional QS genes involved. To address these questions, we performed a metagenomic screen for AHL genes in an activated sludge microbial community from the Ulu Pandan wastewater treatment plant (WWTP) in Singapore followed by functional validation of luxI activity using AHL biosensors and LC–MSMS profiling. We identified 13 luxI and 30 luxR homologs from the activated sludge metagenome. Of those genes, two represented a cognate pair of luxIR genes belonging to a Nitrospira spp. and those genes were demonstrated to be functionally active. The LuxI homolog synthesized AHLs that were consistent with the dominant AHLs in the activated sludge system. Furthermore, the LuxR homolog was shown to bind to and induce expression of the luxI promoter, suggesting this represents an autoinduction feedback system, characteristic of QS circuits. Additionally, a second, active promoter was upstream of a gene encoding a protein with a GGDEF/EAL domain, commonly associated with modulating the intracellular concentration of the secondary messenger, c-di-GMP. Thus, the metagenomic approach used here was demonstrated to effectively identify functional QS genes and suggests that Nitrospira spp. maybe QS is active in the activated sludge community.
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Altaie AM, Saddik B, Alsaegh MA, Soliman SSM, Hamoudi R, Samaranayake LP. Prevalence of unculturable bacteria in the periapical abscess: A systematic review and meta-analysis. PLoS One 2021; 16:e0255485. [PMID: 34351963 PMCID: PMC8341601 DOI: 10.1371/journal.pone.0255485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/18/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To assess the prevalence of unculturable bacteria in periapical abscess, radicular cyst, and periapical granuloma. METHODS PubMed, Scopus, Science Direct, and Ovid databases were systematically searched from January 1990 to May 2020. All the included studies were cross-sectional design. The risk of bias was assessed using Joanna Briggs Institute check-list. Heterogeneity was described using meta-regression and mixed-effects model for lesion, country, and sequence technique moderators. Funnel plot and unweighted Egger's regression test were used to estimate the publication bias. Microbiome data on diversity, abundance, and frequency of unculturable bacteria in the periapical lesions were reviewed, analysed, and the principal component analysis (PCA) was performed. RESULTS A total of 13 studies out of 14,780, were selected for the final analysis. These studies focused on the prevalence of unculturable bacteria in periapical abscesses and related lesions. Approximately 13% (95% CI: 7-23%) of the cumulative number of bacteria derived from periapical abscesses was unculturable. Country moderator significantly (P = 0.05) affects the diversity summary proportion. While the pooled frequency of unculturable bacteria was 8%; 95% CI: 5, 14%, the estimate of the pooled abundance of unculturable bacteria was 5%; 95% CI: 2, 12% with a significant (P = 0.05) country moderator that affects the abundance summary proportion. Of the 62 unculturable bacteria, 35 were subjected to PCA and Peptostreptococcus sp. oral clone CK035 was the most abundant species in periapical abscesses. Hybridization techniques were found to be the most reliable molecular methods in detecting the abundance and frequency of unculturable bacteria. CONCLUSION The significant prevalence of unculturable bacteria in the periapical abscess, suggests that they are likely to play, a yet unknown, critical role in the pathogenesis and progression of the disease. Further research remains to be done to confirm their specific contributions in the virulence and disease progression.
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Affiliation(s)
- Alaa Muayad Altaie
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Basema Saddik
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Family and Community Medicine, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Mohammed Amjed Alsaegh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, UAE
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- * E-mail: (RH); (LPS)
| | - Lakshman P. Samaranayake
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, UAE
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, Sharjah, UAE
- * E-mail: (RH); (LPS)
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11
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Baldewijns S, Sillen M, Palmans I, Vandecruys P, Van Dijck P, Demuyser L. The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis. Front Microbiol 2021; 12:705779. [PMID: 34276639 PMCID: PMC8282898 DOI: 10.3389/fmicb.2021.705779] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.
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Affiliation(s)
- Silke Baldewijns
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Mart Sillen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ilse Palmans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
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12
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Sjövall A, Aho VTE, Hyyrynen T, Kinnari TJ, Auvinen P, Silvola J, Aarnisalo A, Laulajainen-Hongisto A. Microbiome of the Healthy External Auditory Canal. Otol Neurotol 2021; 42:e609-e614. [PMID: 33347052 DOI: 10.1097/mao.0000000000003031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To investigate the microbiota of the healthy external auditory canal (EAC) culture-independently and to evaluate the usefulness of the swabbing method in collecting EAC microbiota samples. STUDY DESIGN Cohort study. PATIENTS Fifty healthy asymptomatic working-age volunteers. INTERVENTION Samples were harvested with DNA-free swabs from the volunteers' EACs. MAIN OUTCOME MEASURES Amplicon sequencing of the 16S rRNA gene was used to characterize the microbial communities in the samples. RESULTS The swabbing method is feasible for EAC microbiota sample collection. The analyzed 41 samples came from 27 female and 14 male subjects; 4 samples were excluded due to recent antimicrobial treatment and 5 because of low sequence count or suspected contaminant microbes. The four most frequent amplicon sequence variants in the microbiota data were Staphylococcus auricularis, Propionibacterium acnes, Alloiococcus otitis, and Turicella otitidis. Typically, the dominant amplicon sequence variant in a sample was one of the most frequent bacteria, but there were also subjects where the dominant species was not among the most frequent ones. The genus Alloiococcus was least common in females who reported cleaning their ears. Subjects with a high relative abundance of Alloiococcus typically had a low abundance of Staphylococcus, which may be a sign of the two being competing members of the microbial community. CONCLUSIONS The most common bacteria in the microbiome of the healthy EAC were Staphylococcus auricularis, Propionibacterium acnes, Alloiococcus otitis, and Turicella otitidis. The EAC microbiota seems more diverse and individualized than previously thought. Also, ear cleaning habits seem to alter the EAC microbiome.
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Affiliation(s)
- Atte Sjövall
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Velma T E Aho
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Taneli Hyyrynen
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Teemu J Kinnari
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki
| | - Juha Silvola
- Department of Otorhinolaryngology, Akershus University Hospital and University of Oslo, Akershus and Oslo, Norway
| | - Antti Aarnisalo
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Anu Laulajainen-Hongisto
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
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The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil. AGRONOMY-BASEL 2021. [DOI: 10.3390/agronomy11040772] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.
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Nousias O, Montesanto F. Metagenomic profiling of host-associated bacteria from 8 datasets of the red alga Porphyra purpurea with MetaPhlAn3. Mar Genomics 2021; 59:100866. [PMID: 33812777 DOI: 10.1016/j.margen.2021.100866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022]
Abstract
Microbial communities play fundamental roles in association with marine algae; in fact, they are recognized to be actively involved in growth and morphogenesis of the algae. Porphyra purpurea is a red alga commonly found in the intertidal zone with a high economic value, however little is known about the bacterial species associated with this genus. Here we report the bacterial-associated diversity of P. purpurea in four different localities (Ireland, Italy United Kingdom and the USA) from analyzing eight publicly available metagenomic datasets. These were analyzed with Methaplan3 to identify the putative bacterial taxonomies and their relative abundances. Furthermore, we compared these results to the 16S rRNA metagenomic analysis pipeline of the MGnify database to evaluate both methods. Kraken2 was used to verify and support the results, as a complementary classification method to Metaphlan3. This approach highlighted the different taxonomic resolution of a 16S rRNA OTU-based method compared to the pan-genome approach deployed by Metaphlan3 and complemented by Kraken2. The results presented here provide valuable preliminary data on the putative host-associated bacterial species of P. purpurea.
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Affiliation(s)
- Orestis Nousias
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Crete, Greece; Department of Biology, University of Crete, Greece.
| | - Federica Montesanto
- Department of Biology, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy; CoNISMa, Piazzale Flaminio 9, 00197 Roma, Italy.
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15
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Hidalgo KJ, Sierra-Garcia IN, Dellagnezze BM, de Oliveira VM. Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain. Front Microbiol 2020; 11:561506. [PMID: 33072021 PMCID: PMC7530279 DOI: 10.3389/fmicb.2020.561506] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 02/01/2023] Open
Abstract
Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.
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Affiliation(s)
- Kelly J. Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabel N. Sierra-Garcia
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
- Biology Department & Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Bruna M. Dellagnezze
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
| | - Valéria Maia de Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Paulínia, Brazil
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16
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An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists. Life (Basel) 2020; 10:life10090185. [PMID: 32911871 PMCID: PMC7555798 DOI: 10.3390/life10090185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 01/02/2023] Open
Abstract
High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.
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17
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Antibacterial Activity of Marine Bacterial Pigments Obtained from Arabian Sea Water Samples. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.1.54] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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18
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Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines. World J Microbiol Biotechnol 2020; 36:51. [PMID: 32157408 DOI: 10.1007/s11274-020-02825-2] [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: 11/15/2019] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.
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19
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Singh H, Kamble A, Sawant S. 16S ribosomal RNA gene-based metagenomics: A review. BIOMEDICAL RESEARCH JOURNAL 2020. [DOI: 10.4103/bmrj.bmrj_4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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20
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Curty G, de Carvalho PS, Soares MA. The Role of the Cervicovaginal Microbiome on the Genesis and as a Biomarker of Premalignant Cervical Intraepithelial Neoplasia and Invasive Cervical Cancer. Int J Mol Sci 2019; 21:ijms21010222. [PMID: 31905652 PMCID: PMC6981542 DOI: 10.3390/ijms21010222] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 12/24/2022] Open
Abstract
The microbiome is able to modulate immune responses, alter the physiology of the human organism, and increase the risk of viral infections and development of diseases such as cancer. In this review, we address changes in the cervical microbiota as potential biomarkers to identify the risk of cervical intraepithelial neoplasia (CIN) development and invasive cervical cancer in the context of human papillomavirus (HPV) infection. Current approaches for clinical diagnostics and the manipulation of microbiota with the use of probiotics and through microbiota transplantation are also discussed.
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21
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Spencer SP, Fragiadakis GK, Sonnenburg JL. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity 2019; 51:225-239. [PMID: 31433970 DOI: 10.1016/j.immuni.2019.08.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant "map" of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.
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Affiliation(s)
- Sean P Spencer
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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22
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Dixon M, Sha S, Stefil M, McDonald M. Is it Time to Say Goodbye to Culture and Sensitivity? The Case for Culture-independent Urology. Urology 2019; 136:112-118. [PMID: 31786305 DOI: 10.1016/j.urology.2019.11.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing has highlighted the limitations of conventional culture methods in the role of urology while discovering the intricate details of the role of microbiota in urologic health and disease. This review article explores: the utility and limitations of conventional culture methods; how culture-independent technologies are revolutionizing medicine; and how the implementation of these technologies may lead to improved patient outcomes. Finally, this article discusses the barriers to widespread adoption of culture-independent technologies, with suggestions for how these hurdles may be overcome.
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Affiliation(s)
- Matthew Dixon
- Norwich Medical School, University of East Anglia, Norwich, UK.
| | - Sybil Sha
- Geisel School of Medicine, Dartmouth College, Hanover, NH
| | - Maria Stefil
- Norwich Medical School, University of East Anglia, Norwich, UK
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23
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Presence of Different Bacterial Species in Thermal Sources and Novelty in Their Industrial Enzyme Productions. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.3.08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Subasinghe R, Samarajeewa A, Scroggins R, Beaudette L. Evaluation of denaturing gradient gel electrophoresis (DGGE) and next generation sequencing (NGS) in combination with enrichment culture techniques to identify bacteria in commercial microbial-based products. J Microbiol Methods 2019; 161:118-130. [DOI: 10.1016/j.mimet.2019.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 11/27/2022]
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25
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Gardner PP, Watson RJ, Morgan XC, Draper JL, Finn RD, Morales SE, Stott MB. Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ 2019; 7:e6160. [PMID: 30631651 PMCID: PMC6322486 DOI: 10.7717/peerj.6160] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 11/14/2018] [Indexed: 01/26/2023] Open
Abstract
Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
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Affiliation(s)
- Paul P Gardner
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Renee J Watson
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jenny L Draper
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Matthew B Stott
- Biomolecular Interactions Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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26
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Kamutando CN, Vikram S, Kamgan-Nkuekam G, Makhalanyane TP, Greve M, Le Roux JJ, Richardson DM, Cowan DA, Valverde A. The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata. MICROBIAL ECOLOGY 2019; 77:191-200. [PMID: 29948018 DOI: 10.1007/s00248-018-1214-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/28/2018] [Indexed: 05/09/2023]
Abstract
Plant-microbe interactions mediate both the invasiveness of introduced plant species and the impacts that they have in invaded ecosystems. Although the phylogenetic composition of the rhizospheric microbiome of Acacia dealbata (an invasive Australian tree species) has been investigated, little is known about the functional potential of the constituents of these altered microbial communities. We used shotgun DNA sequencing to better understand the link between bacterial community composition and functional capacity in the rhizospheric microbiomes associated with invasive A. dealbata populations in South Africa. Our analysis showed that several genes associated with plant growth-promoting (PGP) traits were significantly overrepresented in the rhizospheric metagenomes compared to neighbouring bulk soils collected away from A. dealbata stands. The majority of these genes are involved in the metabolism of nitrogen, carbohydrates and vitamins, and in various membrane transport systems. Overrepresented genes were linked to a limited number of bacterial taxa, mostly Bradyrhizobium species, the preferred N-fixing rhizobial symbiont of Australian acacias. Overall, these findings suggest that A. dealbata enriches rhizosphere soils with potentially beneficial microbial taxa, and that members of the genus Bradyrhizobium may play an integral role in mediating PGP processes that may influence the success of this invader when colonizing novel environments.
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Affiliation(s)
- Casper N Kamutando
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Gilbert Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Michelle Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Johannes J Le Roux
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - David M Richardson
- Centre for Invasion Biology, Department of Botany & Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Angel Valverde
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa.
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, P.O. Box 339, Bloemfontein, Free State, 9300, South Africa.
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Johny TK, Saidumohamed BE, Sasidharan RS, Bhat SG. Inferences of gut bacterial diversity from next-generation sequencing of 16S rDNA in deep sea blind ray - Benthobatis moresbyi. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egg.2018.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Almeida OGG, De Martinis ECP. Bioinformatics tools to assess metagenomic data for applied microbiology. Appl Microbiol Biotechnol 2018; 103:69-82. [DOI: 10.1007/s00253-018-9464-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 12/14/2022]
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Liu Z, Zhang Y, Zhang F, Hu C, Liu G, Pan J. Microbial Community Analyses of the Deteriorated Storeroom Objects in the Tianjin Museum Using Culture-Independent and Culture-Dependent Approaches. Front Microbiol 2018; 9:802. [PMID: 29780363 PMCID: PMC5946025 DOI: 10.3389/fmicb.2018.00802] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
In the storeroom C7 of the Tianjin Museum, one wooden desk and two leather luggages dated back to Qing dynasty (1644-1912 AD) presented viable microbial contamination. The aim of the present study was to investigate microbial communities responsible for the biodeterioration of storeroom objects using a combination of culture-independent and culture-dependent methods as well microscopic techniques. Scanning electron microscopy (SEM) revealed that the microflora on three storeroom objects were characterized by a marked presence of Eurotium halophilicum. Real-time quantitative polymerase chain reaction (qPCR) analysis proved that fungi were the main causative agents behind the biodeterioration in this case. Fungal internal transcribed spacer (ITS) amplicon sequencing documented the presence of two main fungi — Eurotium halophilicum and Aspergillus penicillioides. Molecular identification of fungal strains isolated from the surfaces and the air of the storeroom were most closely related to Chaetomium, Aspergillus, Penicillium, and Fusarium, showing discrepancies in fungal taxa compared to ITS amplicon sequencing. The most isolated bacterial phylum was Firmicutes, mostly Bacillus members. In addition, four biocide products — Preventol® D 7, P 91, 20 N and Euxyl® K 100 were selected to test their capability against fungal strains isolated from the surfaces. According to the susceptibility assay, Preventol® D 7 based on isothiazolinones was the most effective against fungal isolates. Findings from this study provided a knowledge about storeroom fungi, and exemplify a type of preliminary test that may be conducted before planning any biocide treatment, which may be useful to mitigate the fungal deterioration for further conservation of the museum.
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Affiliation(s)
- Zijun Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Fengyu Zhang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cuiting Hu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Jiao Pan
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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The Emergency Medical Service Microbiome. Appl Environ Microbiol 2018; 84:AEM.02098-17. [PMID: 29222105 DOI: 10.1128/aem.02098-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/01/2017] [Indexed: 11/20/2022] Open
Abstract
Emergency medical services (EMS) personnel are an integral component of the health care framework and function to transport patients from various locations to and between care facilities. In addition to physical injury, EMS personnel are expected to be at high risk to acquire and transmit health care-associated infections (HAIs) in the workplace. However, currently, little is known about EMS biosafety risk factors and the epidemiological contribution of EMS to pathogen transmission within and outside the health care sector. Health care facility microbiomes contain diverse bacterial, fungal, and viral pathogens that cause over 1.7 million HAIs each year in the United States alone. While hospital microbiomes have been relatively well studied, there is scant information about EMS infrastructure and equipment microbiomes or the role(s) they play in HAI transmission between health care facilities. We review recent literature investigating the microbiome of ambulances and other EMS service facilities which consistently identify antibiotic-resistant pathogens causing HAIs, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus, and Klebsiella pneumoniae Our review provides evidence that EMS microbiomes are dynamic and important pathogen reservoirs, and it underscores the need for more widespread and in-depth microbiome studies to elucidate patterns of pathogen transmission. We discuss emerging DNA sequencing technologies and other methods that can be applied to characterize and mitigate EMS biosafety risks in the future. Understanding the complex interplay between EMS and hospital microbiomes will provide key insights into pathogen transmission mechanisms and identify strategies to minimize HAIs and community infection.
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31
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Lee MH, Khan R, Tao W, Choi K, Lee SY, Lee JW, Hwang EC, Lee SW. Soil metagenome-derived 3-hydroxypalmitic acid methyl ester hydrolases suppress extracellular polysaccharide production in Ralstonia solanacearum. J Biotechnol 2018; 270:30-38. [PMID: 29407418 DOI: 10.1016/j.jbiotec.2018.01.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 10/18/2022]
Abstract
Autoinducers are indispensable for bacterial cell-cell communication. However, due to the reliance on culture-based techniques, few autoinducer-hydrolyzing enzymes are known. In this study, we characterized soil metagenome-derived unique enzymes capable of hydrolyzing 3-hydroxypalmitic acid methyl ester (3-OH PAME), an autoinducer of the plant pathogenic bacterium Ralstonia solanacearum. Among 146 candidate lipolytic clones from a soil metagenome library, 4 unique enzymes capable of hydrolyzing the autoinducer 3-OH PAME, termed ELP86, ELP96, ELP104, and EstDL33, were selected and characterized. Phylogenetic analysis revealed that metagenomic enzymes were novel esterase/lipase candidates as they clustered as novel subfamilies of family I, V, X, and family XI. The purified enzymes displayed various levels of hydrolytic activities towards 3-OH PAME with optimum activity at 40-50 °C and pH 7-10. Interestingly, ELP104 also displayed N-(3-oxohexanoyl)-L-homoserine lactone hydrolysis activity. Heterologous expression of the gene encoding 3-OH PAME hydrolase in R. solanacearum significantly decreased exopolysaccharide production without affecting bacterial growth. mRNA transcription analysis revealed that genes regulated by quorum-sensing, such as phcA and xpsR, were significantly down-regulated in the stationary growth phase of R. solanacearum. Therefore, metagenomic enzymes are capable of quorum-quenching by hydrolyzing the autoinducer 3-OH PAME, which could be used as a biocontrol strategy against bacterial wilt.
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Affiliation(s)
- Myung Hwan Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Weixin Tao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University, Wuhan, 430072, China
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Jae Wook Lee
- Department of Chemistry, Dong-A University, Busan 49315, Republic of Korea
| | - Eul Chul Hwang
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea.
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32
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Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD. Forgotten fungi-the gut mycobiome in human health and disease. FEMS Microbiol Rev 2017; 41:479-511. [PMID: 28430946 DOI: 10.1093/femsre/fuw047] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our 'mycobiome'. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
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Affiliation(s)
- Chloe E Huseyin
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul W O'Toole
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland.,School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland.,APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
| | - Pauline D Scanlan
- APC Microbiome Institute, Biosciences Institute, University College Cork, Cork T12 YT20 Ireland
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33
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Novello G, Gamalero E, Bona E, Boatti L, Mignone F, Massa N, Cesaro P, Lingua G, Berta G. The Rhizosphere Bacterial Microbiota of Vitis vinifera cv. Pinot Noir in an Integrated Pest Management Vineyard. Front Microbiol 2017; 8:1528. [PMID: 28855895 PMCID: PMC5557794 DOI: 10.3389/fmicb.2017.01528] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022] Open
Abstract
Microorganisms associated with Vitis vinifera (grapevine) can affect its growth, health and grape quality. The aim of this study was to unravel the biodiversity of the bacterial rhizosphere microbiota of grapevine in an integrated pest management vineyard located in Piedmont, Italy. Comparison between the microbial community structure in the bulk and rhizosphere soil (variable: space) were performed. Moreover, the possible shifts of the bulk and rhizosphere soil microbiota according to two phenological stages such as flowering and early fruit development (variable: time) were characterized. The grapevine microbiota was identified using metagenomics and next-generation sequencing. Biodiversity was higher in the rhizosphere than in the bulk soil, independent of the phenological stage. Actinobacteria were the dominant class with frequencies ≥ 50% in all the soil samples, followed by Proteobacteria, Gemmatimonadetes, and Bacteroidetes. While Actinobacteria and Proteobacteria are well-known as being dominant in soil, this is the first time the presence of Gemmatimonadetes has been observed in vineyard soils. Gaiella was the dominant genus of Actinobacteria in all the samples. Finally, the microbiota associated with grapevine differed from the bulk soil microbiota and these variations were independent of the phenological stage of the plant.
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Affiliation(s)
- Giorgia Novello
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Elisa Bona
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Lara Boatti
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy.,SmartSeq s.r.l.Alessandria, Italy
| | - Flavio Mignone
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy.,SmartSeq s.r.l.Alessandria, Italy
| | - Nadia Massa
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Patrizia Cesaro
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Guido Lingua
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
| | - Graziella Berta
- Dipartimento di Scienze e Innovazione Tecnologica, Università degli Studi del Piemonte OrientaleAlessandria, Italy
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34
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Doyle CJ, Gleeson D, O'Toole PW, Cotter PD. High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions. Int J Food Microbiol 2017; 255:1-6. [DOI: 10.1016/j.ijfoodmicro.2017.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/16/2017] [Accepted: 05/21/2017] [Indexed: 12/20/2022]
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35
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Li Y, Zhang J, Zhang Y, Quan X. Scaling-up of a zero valent iron packed anaerobic reactor for textile dye wastewater treatment: a potential technology for on-site upgrading and rebuilding of traditional anaerobic wastewater treatment plant. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2017; 76:823-831. [PMID: 28799929 DOI: 10.2166/wst.2017.270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Anaerobic digestion (AD) is a cost-effective technology for the treatment of textile dye wastewater with clear environmental benefits. However, the need to improve process feasibility of high treatment efficiency as well as to shorten hydraulic retention time has raised interest on several intensification techniques. Zero valent iron (ZVI) packed anaerobic digesters have the potential to become an on-site upgrading wastewater treatment technology through building a ZVI bed in a traditional AD plant. However, the experiences and knowledge of scale-up are limited. In this study, a pilot-scale ZVI packed upflow anaerobic sludge bed (ZVI-UASB) was built up and operated for actual dye wastewater treatment in a textile dye industrial park. Results showed that the treatment performance of this digester is higher than that of a traditional AD plant in terms of chemical oxygen demand (COD) removal and color removal. During 90 days of operation, the average COD removal and color removal in ZVI-UASB was maintained at around 19% and 40%, respectively, while it was only 10% and 20%, respectively, in the traditional AD plant.
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Affiliation(s)
- Yang Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China E-mail:
| | - Jingxin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China E-mail: ; NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China E-mail:
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China E-mail:
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36
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Rapid and efficient method to extract metagenomic DNA from estuarine sediments. 3 Biotech 2017; 7:182. [PMID: 28664369 DOI: 10.1007/s13205-017-0846-y] [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] [Received: 04/20/2017] [Accepted: 05/24/2017] [Indexed: 10/19/2022] Open
Abstract
Metagenomic DNA from sediments of selective estuaries of Goa, India was extracted using a simple, fast, efficient and environment friendly method. The recovery of pure metagenomic DNA from our method was significantly high as compared to other well-known methods since the concentration of recovered metagenomic DNA ranged from 1185.1 to 4579.7 µg/g of sediment. The purity of metagenomic DNA was also considerably high as the ratio of absorbance at 260 and 280 nm ranged from 1.88 to 1.94. Therefore, the recovered metagenomic DNA was directly used to perform various molecular biology experiments viz. restriction digestion, PCR amplification, cloning and metagenomic library construction. This clearly proved that our protocol for metagenomic DNA extraction using silica gel efficiently removed the contaminants and prevented shearing of the metagenomic DNA. Thus, this modified method can be used to recover pure metagenomic DNA from various estuarine sediments in a rapid, efficient and eco-friendly manner.
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Clemmons BA, Reese ST, Dantas FG, Franco GA, Smith TPL, Adeyosoye OI, Pohler KG, Myer PR. Vaginal and Uterine Bacterial Communities in Postpartum Lactating Cows. Front Microbiol 2017. [PMID: 28642755 PMCID: PMC5463355 DOI: 10.3389/fmicb.2017.01047] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reproductive inefficiency in cattle has major impacts on overall productivity of cattle operations, increasing cost of production, and impacting the sustainability of the cattle enterprise. Decreased reproductive success and associated disease states have been correlated with the presence of specific microbes and microbial community profiles, yet details of the relationship between microbial communities and host physiology are not well known. The present study profiles and compares the microbial communities in the bovine uterus and vagina using 16S rRNA sequencing of the V1-V3 hypervariable region at the time of artificial insemination. Significant differences (p < 0.05) between the vaginal and uterine communities were observed at the level of α-diversity metrics, including Chao1, Shannon's Diversity Index, and observed OTU. Greater clustering of vaginal OTU was apparent in principal coordinate analysis compared to uterine OTU, despite greater diversity in the vaginal community in both weighted and unweighted UniFrac distance matrices (p < 0.05). There was a significantly greater relative abundance of unassigned taxa in the uterus (p = 0.008), otherwise there were few differences between the overall community profiles. Both vaginal and uterine communities were dominated by Firmicutes, although the relative abundance of rRNA sequences corresponding to species in this phylum was significantly (p = 0.007) lower in the uterine community. Additional differences were observed at the genus level, specifically in abundances within Clostridium (p = 0.009), Anaerofustis (p = 0.018), Atopobium (p = 0.035), Oscillospira (p = 0.035), 5-7N15 (p = 0.035), Mycoplasma (p = 0.035), Odoribacter (p = 0.042), and within the families Clostridiaceae (p = 0.006), Alcaligenaceae (p = 0.021), and Ruminococcaceae (p = 0.021). Overall, the comparison revealed differences and commonalities among bovine reproductive organs, which may be influenced by host physiology. The increased abundance of unassigned taxa found in the uterus may play a significant biological role in the reproductive status of the animal. The study represents an initial dataset for comparing bacterial communities prior to establishment of pregnancy.
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Affiliation(s)
- Brooke A Clemmons
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
| | - Sydney T Reese
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
| | - Felipe G Dantas
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
| | - Gessica A Franco
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
| | - Timothy P L Smith
- U.S. Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture, Clay Center, NEUnited States
| | | | - Ky G Pohler
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
| | - Phillip R Myer
- University of Tennessee Institute of Agriculture, University of Tennessee, KnoxvilleTN, United States
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38
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Hayes S, Mahony J, Nauta A, van Sinderen D. Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Viruses 2017; 9:v9060127. [PMID: 28538703 PMCID: PMC5490804 DOI: 10.3390/v9060127] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/18/2017] [Accepted: 05/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacteriophages are ubiquitous and numerous parasites of bacteria and play a critical evolutionary role in virtually every ecosystem, yet our understanding of the extent of the diversity and role of phages remains inadequate for many ecological niches, particularly in cases in which the host is unculturable. During the past 15 years, the emergence of the field of viral metagenomics has drastically enhanced our ability to analyse the so-called viral ‘dark matter’ of the biosphere. Here, we review the evolution of viral metagenomic methodologies, as well as providing an overview of some of the most significant applications and findings in this field of research.
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Affiliation(s)
- Stephen Hayes
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
| | - Arjen Nauta
- Friesland Campina, Amersfoort 3800 BN, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork T12 YT20, Ireland.
- APC Microbiome Institute, University College Cork, Cork T12 YT20, Ireland.
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39
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Ashrafi M, Baguneid M, Alonso-Rasgado T, Rautemaa-Richardson R, Bayat A. Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome. Future Microbiol 2017; 12:337-357. [DOI: 10.2217/fmb-2016-0204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Infection contributes significantly to delayed cutaneous wound healing, which impacts patient care. External application of electrical stimulation (ES) has beneficial effects on wound repair and regeneration. The majority of studies to date have explored ES in relation to planktonic microorganisms, yet evidence indicates that bacteria in chronic wounds reside as antibiotic-resistant polymicrobial biofilms, which contribute to impairing wound healing. Culture-independent sequencing techniques have revolutionized our understanding of the skin microbiome and allowed a more accurate determination of microbial taxa and their relative abundance in wounds allowing a greater understanding of the host–microbial interface. Future studies combining the fields of ES, biofilm and microbiome research are necessary to fully elucidate the use of ES in the management of wound infection.
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Affiliation(s)
- Mohammed Ashrafi
- Plastic & Reconstructive Surgery Research, Centre for Dermatological Research, University of Manchester, Manchester, UK
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Bioengineering Group, School of Materials, University of Manchester, Manchester, UK
| | - Mohamed Baguneid
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
| | | | - Riina Rautemaa-Richardson
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Manchester Academic Health Science Centre, Institute of Inflammation & Repair, University of Manchester, Manchester, UK
| | - Ardeshir Bayat
- Plastic & Reconstructive Surgery Research, Centre for Dermatological Research, University of Manchester, Manchester, UK
- University Hospital of South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
- Bioengineering Group, School of Materials, University of Manchester, Manchester, UK
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40
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Hartman K, van der Heijden MG, Roussely-Provent V, Walser JC, Schlaeppi K. Deciphering composition and function of the root microbiome of a legume plant. MICROBIOME 2017; 5:2. [PMID: 28095877 PMCID: PMC5240445 DOI: 10.1186/s40168-016-0220-z] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/08/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is available for legumes despite their key role in numerous ecosystems including agricultural systems. Legumes form a root nodule symbiosis with nitrogen-fixing Rhizobia bacteria and thereby account for large, natural nitrogen inputs into soils. Here, we describe the root bacteria microbiome of the legume Trifolium pratense combining culture-dependent and independent methods. For a functional understanding of individual microbiome members and their impact on plant growth, we began to inoculate root microbiome members alone or in combination to Trifolium roots. RESULTS At a whole-root scale, Rhizobia bacteria accounted for ~70% of the root microbiome. Other enriched members included bacteria from the genera Pantoea, Sphingomonas, Novosphingobium, and Pelomonas. We built a reference stock of 200 bacteria isolates, and we found that they corresponded to ~20% of the abundant root microbiome members. We developed a microcosm system to conduct simplified microbiota inoculation experiments with plants. We observed that while an abundant root microbiome member reduced plant growth when inoculated alone, this negative effect was alleviated if this Flavobacterium was co-inoculated with other root microbiome members. CONCLUSIONS The Trifolium root microbiome was dominated by nutrient-providing Rhizobia bacteria and enriched for bacteria from genera that may provide disease protection. First microbiota inoculation experiments indicated that individual community members can have plant growth compromising activities without being apparently pathogenic, and a more diverse root community can alleviate plant growth compromising activities of its individual members. A trait-based characterization of the reference stock bacteria will permit future microbiota manipulation experiments to decipher overall microbiome functioning and elucidate the biological mechanisms and interactions driving the observed effects. The presented reductionist experimental approach offers countless opportunities for future systematic and functional examinations of the plant root microbiome.
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Affiliation(s)
- Kyle Hartman
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department for Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Marcel Ga van der Heijden
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department for Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | | | - Klaus Schlaeppi
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
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41
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Rahman SJ, Charles TC, Kaur P. Metagenomic Approaches to Identify Novel Organisms from the Soil Environment in a Classroom Setting. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2016; 17:423-429. [PMID: 28101269 PMCID: PMC5134946 DOI: 10.1128/jmbe.v17i3.1115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Molecular Microbial Metagenomics is a research-based undergraduate course developed at Georgia State University. This semester-long course provides hands-on research experience in the area of microbial diversity and introduces molecular approaches to study diversity. Students are part of an ongoing research project that uses metagenomic approaches to isolate clones containing 16S ribosomal ribonucleic acid (rRNA) genes from a soil metagenomic library. These approaches not only provide a measure of microbial diversity in the sample but may also allow discovery of novel organisms. Metagenomic approaches differ from the traditional culturing methods in that they use molecular analysis of community deoxyribonucleic acid (DNA) instead of culturing individual organisms. Groups of students select a batch of 100 clones from a metagenomic library. Using universal primers to amplify 16S rRNA genes from the pool of DNA isolated from 100 clones, and a stepwise process of elimination, each group isolates individual clones containing 16S rRNA genes within their batch of 100 clones. The amplified 16S rRNA genes are sequenced and analyzed using bioinformatics tools to determine whether the rRNA gene belongs to a novel organism. This course provides avenues for active learning and enhances students' conceptual understanding of microbial diversity. Average scores on six assessment methods used during field testing indicated that success in achieving different learning objectives varied between 84% and 95%, with 65% of the students demonstrating complete grasp of the project based on the end-of-project lab report. The authentic research experience obtained in this course is also expected to result in more undergraduates choosing research-based graduate programs or careers.
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Affiliation(s)
- Sadia J. Rahman
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON N2V 2P1, Canada
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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Krishnan K, Chen T, Paster BJ. A practical guide to the oral microbiome and its relation to health and disease. Oral Dis 2016; 23:276-286. [PMID: 27219464 DOI: 10.1111/odi.12509] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/14/2022]
Abstract
The oral microbiome is incredibly complex with the average adult harboring about 50-100 billion bacteria in the oral cavity, which represent about 200 predominant bacterial species. Collectively, there are approximately 700 predominant taxa of which less than one-third still have not yet been grown in vitro. Compared to other body sites, the oral microbiome is unique and readily accessible. There is extensive literature available describing the oral microbiome and discussing the roles that bacteria may play in oral health and disease. However, the purpose of this review is not to rehash these detailed studies but rather to educate the reader with understanding the essence of the oral microbiome, namely that there are abundant bacteria in numbers and types, that there are molecular methods to rapidly determine bacterial associations, that there is site specificity for colonization of the host, that there are specific associations with oral health and disease, that oral bacteria may serve as biomarkers for non-oral diseases, and that oral microbial profiles may have potential use to assess disease risk.
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Affiliation(s)
- K Krishnan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,New England BioLabs, Ipswich, MA, USA
| | - T Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - B J Paster
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection & Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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Thiel V, Wood JM, Olsen MT, Tank M, Klatt CG, Ward DM, Bryant DA. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing. Front Microbiol 2016; 7:919. [PMID: 27379049 PMCID: PMC4911352 DOI: 10.3389/fmicb.2016.00919] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/27/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial-mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin at Yellowstone National Park have been studied for nearly 50 years. The emphasis has mostly focused on the chlorophototrophic bacterial organisms of the phyla Cyanobacteria and Chloroflexi. In contrast, the diversity and metabolic functions of the heterotrophic community in the microoxic/anoxic region of the mat are not well understood. In this study we analyzed the orange-colored undermat of the microbial community of Mushroom Spring using metagenomic and rRNA-amplicon (iTag) analyses. Our analyses disclosed a highly diverse community exhibiting a high degree of unevenness, strongly dominated by a single taxon, the filamentous anoxygenic phototroph, Roseiflexus spp. The second most abundant organisms belonged to the Thermotogae, which have been hypothesized to be a major source of H2 from fermentation that could enable photomixotrophic metabolism by Chloroflexus and Roseiflexus spp. Other abundant organisms include two members of the Armatimonadetes (OP10); Thermocrinis sp.; and phototrophic and heterotrophic members of the Chloroflexi. Further, an Atribacteria (OP9/JS1) member; a sulfate-reducing Thermodesulfovibrio sp.; a Planctomycetes member; a member of the EM3 group tentatively affiliated with the Thermotogae, as well as a putative member of the Arminicenantes (OP8) represented ≥1% of the reads. Archaea were not abundant in the iTag analysis, and no metagenomic bin representing an archaeon was identified. A high microdiversity of 16S rRNA gene sequences was identified for the dominant taxon, Roseiflexus spp. Previous studies demonstrated that highly similar Synechococcus variants in the upper layer of the mats represent ecological species populations with specific ecological adaptations. This study suggests that similar putative ecotypes specifically adapted to different niches occur within the undermat community, particularly for Roseiflexus spp.
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Affiliation(s)
- Vera Thiel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Jason M Wood
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Millie T Olsen
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA
| | - Christian G Klatt
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA; Agricultural Research Service, United States Department of Agriculture, University of MinnesotaSaint Paul, MN, USA
| | - David M Ward
- Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA; Department of Chemistry and Biochemistry, Montana State UniversityBozeman, MT, USA
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Kong HG, Kim NH, Lee SY, Lee SW. Impact of a Recombinant Biocontrol Bacterium, Pseudomonas fluorescens pc78, on Microbial Community in Tomato Rhizosphere. THE PLANT PATHOLOGY JOURNAL 2016; 32:136-44. [PMID: 27147933 PMCID: PMC4853103 DOI: 10.5423/ppj.oa.08.2015.0172] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/16/2015] [Accepted: 11/22/2015] [Indexed: 05/11/2023]
Abstract
Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.
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Affiliation(s)
| | | | | | - Seon-Woo Lee
- Corresponding author. Phone) +82-51-200-7551, FAX) +82-51-200-7505, E-mail)
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Brown SP, Ferrer A, Dalling JW, Heath KD. Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array. Mol Ecol Resour 2016; 16:946-56. [PMID: 26849494 DOI: 10.1111/1755-0998.12507] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 01/24/2023]
Abstract
With the increasing democratization of high-throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community-wide sequencing effort. Here, we use Fluidigm's microfluidic Access Arrays (IFC) followed by Illumina(®) MiSeq Nano sequencing on a culture-derived local mock community to demonstrate how this approach allows for a low-cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.
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Affiliation(s)
- Shawn P Brown
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
| | - Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, 505 S Goodwin Ave., Urbana, IL, 61801, USA
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Kaur G, Sharma R, Singh K, Sharma PK. Delineating bacterial community structure of polluted soil samples collected from cancer prone belt of Punjab, India. 3 Biotech 2015; 5:727-734. [PMID: 28324527 PMCID: PMC4569629 DOI: 10.1007/s13205-014-0270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/13/2014] [Indexed: 11/01/2022] Open
Abstract
16S rRNA gene analysis has emerged as one of the valuable tools that are being utilized in investigating the molecular phylogenetic structure of the particular environment. Here, we embarked upon understanding and delineating the molecular phylogeny structure of microbes in polluted soil samples from cancer prone belt of the Punjab, India, which is highly contaminated with herbicide, pesticide and heavy metals. To investigate the bacterial phylogeny structure, a high-molecular weight metagenomic DNA was extracted from the soil samples, followed by PCR amplification, cloning and analysis of the 16S rRNA genes. Study employing 16S rRNA profiling of the community DNA revealed the presence of two major phylums: the Proteobacteria (26.7 %), the Bacteroidetes (11.2 %), and several minor groups, i.e., Acidobacteria (4.2 %), Actinobacteria (4.2 %), Firmicutes (2.8 %), Verrucomicrobia (2.8 %), Gemmatimonadetes (1.4 %) and Chloroflexi (1.4 %). Among the Proteobacteria, we mainly observed the α-Proteobacteria (18.3 %). Nearly, 38 % of the recovered 16S rRNA gene sequences in this study do not share similarity with known culturable bacterial sequences reported in the genebank data base and hence considered to be novel. More interestingly, 16S rRNA gene sequences of archaeal origin (7.0 %) were also recovered that primarily indicate change in their evolution pattern. A phylogenetic tree constructed based on alignment-dependent method revealed the extent of similarity these clones shared with each other, followed by alignment-independent methods that statistically confirmed the sequence variation among the clones. Despite the high level of contamination in the study area, we observed remarkable microbial diversity that mainly includes the Gram-negative bacteria. The presence of more Gram-negative bacteria indicates that they have evolved a robust mechanism to resist and cope up with these pollutants compared to Gram-positive groups. Investigation of the polluted soil samples employing culture-independent approach revealed important bacterial groups which could be engineered for future bioremediation studies.
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Affiliation(s)
- Gagandeep Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India
| | | | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Pushpender K Sharma
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Pb, India.
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Vaughan MJ, Nelson W, Soderlund C, Maier RM, Pryor BM. Assessing fungal community structure from mineral surfaces in Kartchner Caverns using multiplexed 454 pyrosequencing. MICROBIAL ECOLOGY 2015; 70:175-187. [PMID: 25608778 DOI: 10.1007/s00248-014-0560-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 12/23/2014] [Indexed: 06/04/2023]
Abstract
Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium sequencing technology using the Internal Transcribed Spacer 1 as a fungal barcode marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces, and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2,219 fungal operational taxonomic units (OTUs) at the 95% similarity level. Speleothems supported a higher fungal richness and diversity than rock walls. However, community membership and the taxonomic distribution of fungal OTUs at the class level did not differ significantly between speleothems and rock walls. Both OTU richness and diversity decreased significantly with increasing distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs also differed significantly between the sampling sites closest to the entrance and those furthest away. There was no significant effect of temperature, CO2 concentration, or drip water nutrient concentration on fungal community structure on either speleothems or rock walls. Together, these results suggest that proximity to the natural entrance is a critical factor in determining fungal community structure on mineral surfaces in Kartchner Caverns.
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Mazaheri Assadi M, Chamanrokh P, Whitehouse CA, Huq A. Methods for Detecting the Environmental Coccoid Form of Helicobacter pylori. Front Public Health 2015; 3:147. [PMID: 26075197 PMCID: PMC4446911 DOI: 10.3389/fpubh.2015.00147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/08/2015] [Indexed: 12/29/2022] Open
Abstract
Helicobacter pylori is recognized as the most common pathogen to cause gastritis, peptic and duodenal ulcers, and gastric cancer. The organisms are found in two forms: (1) spiral-shaped bacillus and (2) coccoid. H. pylori coccoid form, generally found in the environment, is the transformed form of the normal spiral-shaped bacillus after exposed to water or adverse environmental conditions such as exposure to sub-inhibitory concentrations of antimicrobial agents. The putative infectious capability and the viability of H. pylori under environmental conditions are controversial. This disagreement is partially due to the fact of lack in detecting the coccoid form of H. pylori in the environment. Accurate and effective detection methods of H. pylori will lead to rapid treatment and disinfection, and less human health damages and reduction in health care costs. In this review, we provide a brief introduction to H. pylori environmental coccoid forms, their transmission, and detection methods. We further discuss the use of these detection methods including their accuracy and efficiency.
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Affiliation(s)
- Mahnaz Mazaheri Assadi
- Environmental Biotechnology Group, Biotechnology Department, Iranian Research Organization for Science and Technology , Tehran , Iran
| | - Parastoo Chamanrokh
- Maryland Pathogen Research Institute, University of Maryland , College Park, MD , USA
| | | | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland , College Park, MD , USA
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50
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