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Jagadesh M, Dash M, Kumari A, Singh SK, Verma KK, Kumar P, Bhatt R, Sharma SK. Revealing the hidden world of soil microbes: Metagenomic insights into plant, bacteria, and fungi interactions for sustainable agriculture and ecosystem restoration. Microbiol Res 2024; 285:127764. [PMID: 38805978 DOI: 10.1016/j.micres.2024.127764] [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: 11/30/2023] [Revised: 03/10/2024] [Accepted: 05/11/2024] [Indexed: 05/30/2024]
Abstract
The future of agriculture is questionable under the current climate change scenario. Climate change and climate-related calamities directly influence biotic and abiotic factors that control agroecosystems, endangering the safety of the world's food supply. The intricate interactions between soil microorganisms, including plants, bacteria, and fungi, play a pivotal role in promoting sustainable agriculture and ecosystem restoration. Soil microbes play a major part in nutrient cycling, including soil organic carbon (SOC), and play a pivotal function in the emission and depletion of greenhouse gases, including CH4, CO2, and N2O, which can impact the climate. At this juncture, developing a triumphant metagenomics approach has greatly increased our knowledge of the makeup, functionality, and dynamics of the soil microbiome. Currently, the involvement of plants in climate change indicates that they can interact with the microbial communities in their environment to relieve various stresses through the innate microbiome assortment of focused strains, a phenomenon dubbed "Cry for Help." The metagenomics method has lately appeared as a new platform to adjust and encourage beneficial communications between plants and microbes and improve plant fitness. The metagenomics of soil microbes can provide a powerful tool for designing and evaluating ecosystem restoration strategies that promote sustainable agriculture under a changing climate. By identifying the specific functions and activities of soil microbes, we can develop restoration programs that support these critical components of healthy ecosystems while providing economic benefits through ecosystem services. In the current review, we highlight the innate functions of microbiomes to maintain the sustainability of agriculture and ecosystem restoration. Through this insight study of soil microbe metagenomics, we pave the way for innovative strategies to address the pressing challenges of food security and environmental conservation. The present article elucidates the mechanisms through which plants and microbes communicate to enhance plant resilience and ecosystem restoration and to leverage metagenomics to identify and promote beneficial plant-microbe interactions. Key findings reveal that soil microbes are pivotal in nutrient cycling, greenhouse gas modulation, and overall ecosystem health, offering novel insights into designing ecosystem restoration strategies that bolster sustainable agriculture. As this is a topic many are grappling with, hope these musings will provide people alike with some food for thought.
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Affiliation(s)
- M Jagadesh
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Munmun Dash
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Aradhna Kumari
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India.
| | - Santosh Kumar Singh
- Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, India.
| | - Krishan K Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Nanning, Guangxi 530007, China.
| | - Prasann Kumar
- Department of Agronomy, School of Agriculture, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Rajan Bhatt
- Krishi Vigyan Kendra, Amritsar, Punjab Agricultural University (PAU), Ludhiana, Punjab 144601, India
| | - Satish Kumar Sharma
- College of Agriculture, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Ganj Basoda, Vidisha, Madhya Pradesh, India
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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [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: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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Orel N, Fadeev E, Herndl GJ, Turk V, Tinta T. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics 2024; 25:146. [PMID: 38321410 PMCID: PMC10845552 DOI: 10.1186/s12864-024-10062-2] [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: 01/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. RESULTS We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. CONCLUSIONS Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
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Matias LLR, Damasceno KSFDSC, Pereira AS, Passos TS, Morais AHDA. Innovative Biomedical and Technological Strategies for the Control of Bacterial Growth and Infections. Biomedicines 2024; 12:176. [PMID: 38255281 PMCID: PMC10813423 DOI: 10.3390/biomedicines12010176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Antibiotics comprise one of the most successful groups of pharmaceutical products. Still, they have been associated with developing bacterial resistance, which has become one of the most severe problems threatening human health today. This context has prompted the development of new antibiotics or co-treatments using innovative tools to reverse the resistance context, combat infections, and offer promising antibacterial therapy. For the development of new alternatives, strategies, and/or antibiotics for controlling bacterial growth, it is necessary to know the target bacteria, their classification, morphological characteristics, the antibiotics currently used for therapies, and their respective mechanisms of action. In this regard, genomics, through the sequencing of bacterial genomes, has generated information on diverse genetic resources, aiding in the discovery of new molecules or antibiotic compounds. Nanotechnology has been applied to propose new antimicrobials, revitalize existing drug options, and use strategic encapsulating agents with their biochemical characteristics, making them more effective against various bacteria. Advanced knowledge in bacterial sequencing contributes to the construction of databases, resulting in advances in bioinformatics and the development of new antimicrobials. Moreover, it enables in silico antimicrobial susceptibility testing without the need to cultivate the pathogen, reducing costs and time. This review presents new antibiotics and biomedical and technological innovations studied in recent years to develop or improve natural or synthetic antimicrobial agents to reduce bacterial growth, promote well-being, and benefit users.
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Affiliation(s)
- Lídia Leonize Rodrigues Matias
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | | | - Annemberg Salvino Pereira
- Nutrition Course, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | - Thaís Souza Passos
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
| | - Ana Heloneida de Araujo Morais
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
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Gumerov VM, Ulrich LE, Zhulin IB. MiST 4.0: a new release of the microbial signal transduction database, now with a metagenomic component. Nucleic Acids Res 2024; 52:D647-D653. [PMID: 37791884 PMCID: PMC10767990 DOI: 10.1093/nar/gkad847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Signal transduction systems in bacteria and archaea link environmental stimuli to specific adaptive cellular responses. They control gene expression, motility, biofilm formation, development and other processes that are vital to survival. The microbial signal transduction (MiST) database is an online resource that stores tens of thousands of genomes and allows users to explore their signal transduction profiles, analyze genomes in bulk using the database application programming interface (API) and make testable hypotheses about the functions of newly identified signaling systems. However, signal transduction in metagenomes remained completely unexplored. To lay the foundation for research in metagenomic signal transduction, we have prepared a new release of the MiST database, MiST 4.0, which features over 10 000 metagenome-assembled genomes (MAGs), a scaled representation of proteins and detailed BioSample information. In addition, several thousands of new genomes have been processed and stored in the database. A new interface has been developed that allows users to seamlessly switch between genomes and MAGs. MiST 4.0 is freely available at https://mistdb.com; metagenomes and MAGs can also be explored using the API available on the same page.
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Affiliation(s)
- Vadim M Gumerov
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | | | - Igor B Zhulin
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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Wani AK, Chopra C, Dhanjal DS, Akhtar N, Singh H, Bhau P, Singh A, Sharma V, Pinheiro RSB, Américo-Pinheiro JHP, Singh R. Metagenomics in the fight against zoonotic viral infections: A focus on SARS-CoV-2 analogues. J Virol Methods 2024; 323:114837. [PMID: 37914040 DOI: 10.1016/j.jviromet.2023.114837] [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: 09/15/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Zoonotic viral infections continue to pose significant threats to global public health, as highlighted by the COVID-19 pandemic caused by the SARS-CoV-2 virus. The emergence of SARS-CoV-2 served as a stark reminder of the potential for zoonotic transmission of viruses from animals to humans. Understanding the origins and dynamics of zoonotic viruses is critical for early detection, prevention, and effective management of future outbreaks. Metagenomics has emerged as a powerful tool for investigating the virome of diverse ecosystems, shedding light on the diversity of viral populations, their hosts, and potential zoonotic spillover events. We provide an in-depth examination of metagenomic approaches, including, NGS metagenomics, shotgun metagenomics, viral metagenomics, and single-virus metagenomics, highlighting their strengths and limitations in identifying and characterizing zoonotic viral pathogens. This review underscores the pivotal role of metagenomics in enhancing our ability to detect, monitor, and mitigate zoonotic viral infections, using SARS-CoV-2 analogues as a case study. We emphasize the need for continued interdisciplinary collaboration among virologists, ecologists, and bioinformaticians to harness the full potential of metagenomic approaches in safeguarding public health against emerging zoonotic threats.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Daljeet Singh Dhanjal
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Himanshu Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Poorvi Bhau
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Anjuvan Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India
| | - Varun Sharma
- NMC Genetics India Pvt. Ltd, Gurugram, Harayana, India
| | - Rafael Silvio Bonilha Pinheiro
- School of Veterinary Medicine and Animal Science, Department of Animal Production, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Juliana Heloisa Pinê Américo-Pinheiro
- Department of Forest Science, Soils and Environment, School of Agronomic Sciences, São Paulo State University (UNESP), Ave. Universitária, 3780, Botucatu, SP 18610-034, Brazil; Graduate Program in Environmental Sciences, Brazil University, Street Carolina Fonseca, 584, São Paulo, SP 08230-030, Brazil
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab 144411, India.
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Soong YHV, Abid U, Chang AC, Ayafor C, Patel A, Qin J, Xu J, Lawton C, Wong HW, Sobkowicz MJ, Xie D. Enzyme selection, optimization, and production toward biodegradation of post-consumer poly(ethylene terephthalate) at scale. Biotechnol J 2023; 18:e2300119. [PMID: 37594123 DOI: 10.1002/biot.202300119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the world's most widely used polyester plastics. Due to its chemical stability, PET is extremely difficult to hydrolyze in a natural environment. Recent discoveries in new polyester hydrolases and breakthroughs in enzyme engineering strategies have inspired enormous research on biorecycling of PET. This study summarizes our research efforts toward large-scale, efficient, and economical biodegradation of post-consumer waste PET, including PET hydrolase selection and optimization, high-yield enzyme production, and high-capacity enzymatic degradation of post-consumer waste PET. First, genes encoding PETase and MHETase from Ideonella sakaiensis and the ICCG variant of leaf-branch compost cutinase (LCCICCG ) were codon-optimized and expressed in Escherichia coli BL21(DE3) for high-yield production. To further lower the enzyme production cost, a pelB leader sequence was fused to LCCICCG so that the enzyme can be secreted into the medium to facilitate recovery. To help bind the enzyme on the hydrophobic surface of PET, a substrate-binding module in a polyhydroxyalkanoate depolymerase from Alcaligenes faecalis (PBM) was fused to the C-terminus of LCCICCG . The resulting four different LCCICCG variants (LCC, PelB-LCC, LCC-PBM, and PelB-LCC-PBM), together with PETase and MHETase, were compared for PET degradation efficiency. A fed-batch fermentation process was developed to produce the target enzymes up to 1.2 g L-1 . Finally, the best enzyme, PelB-LCC, was selected and used for the efficient degradation of 200 g L-1 recycled PET in a well-controlled, stirred-tank reactor. The results will help develop an economical and scalable biorecycling process toward a circular PET economy.
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Affiliation(s)
- Ya-Hue Valerie Soong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Umer Abid
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Allen C Chang
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Christian Ayafor
- Energy Engineering Program, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Akanksha Patel
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Jin Xu
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Carl Lawton
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Hsi-Wu Wong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Margaret J Sobkowicz
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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Kim HY, Kim TH, Shin JH, Cho K, Ha HK, Lee A, Kim YJ. Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change? PeerJ 2023; 11:e16366. [PMID: 38025669 PMCID: PMC10676715 DOI: 10.7717/peerj.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Background We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis. Methods We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used. Results Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups. Conclusion Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.
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Affiliation(s)
- Hee Yeon Kim
- Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Tae Hyun Kim
- Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine and Paik Institute for Clinical Research, Inje University, Busan, South Korea
| | - Kwangrae Cho
- Department of Anesthesiology and Pain Medicine, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Heon-Kyun Ha
- Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea
| | - Anbok Lee
- Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Medical Center, Seoul, South Korea
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Cai H, Zhou Y, Li X, Xu T, Ni Y, Wu S, Yu Y, Wang Y. Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake. Viruses 2023; 15:2038. [PMID: 37896815 PMCID: PMC10611076 DOI: 10.3390/v15102038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.
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Affiliation(s)
- Haoyun Cai
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yifan Zhou
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Xiefei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Tianqi Xu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yimin Ni
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Shuang Wu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongxin Yu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
| | - Yongjie Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China; (H.C.); (Y.Z.); (X.L.); (T.X.); (Y.N.); (S.W.); (Y.Y.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture and Rural Affairs, Shanghai 201306, China
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Singh Y, Rani J, Kushwaha J, Priyadarsini M, Pandey KP, Sheth PN, Yadav SK, Mahesh MS, Dhoble AS. Scientific characterization methods for better utilization of cattle dung and urine: a concise review. Trop Anim Health Prod 2023; 55:274. [PMID: 37470864 DOI: 10.1007/s11250-023-03691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Cattle are usually raised for food, manure, leather, therapeutic, and draught purposes. Biowastes from cattle, such as dung and urine, harbor a diverse group of crucial compounds, metabolites/chemicals, and microorganisms that may benefit humans for agriculture, nutrition, therapeutics, industrial, and other utility products. Several bioactive compounds have been identified in cattle dung and urine, which possess unique properties and may vary based on agro-climatic zones and feeding practices. Therefore, cattle dung and urine have great significance, and a balanced nutritional diet may be a key to improved quality of these products/by-products. This review primarily focuses on the scientific aspects of biochemical and microbial characterization of cattle biowastes. Various methods including genomics for analyzing cattle dung and gas chromatography-mass spectroscopy for cattle urine have been reviewed. The presented information might open doors for the further characterization of cattle resources for heterogeneous applications in the production of utility items and addressing research gaps. Methods for cattle's dung and urine characterization.
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Affiliation(s)
- Yashpal Singh
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Jyoti Rani
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Jeetesh Kushwaha
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Madhumita Priyadarsini
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Kailash Pati Pandey
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India
| | - Pratik N Sheth
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - Sushil Kumar Yadav
- Department of Pharmacy, Birla Institute of Technology and Science (BITS), Pilani, 333031, Rajasthan, India
| | - M S Mahesh
- Livestock Farm Complex, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Rajiv Gandhi South Campus, Mirzapur, 231001, Uttar Pradesh, India
| | - Abhishek S Dhoble
- School of Biochemical Engineering, Indian Institute of Technology (BHU) Varanasi, Uttar Pradesh, 221005, Varanasi, India.
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11
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Santiago BCF, de Souza ID, Cavalcante JVF, Morais DAA, da Silva MB, Pasquali MADB, Dalmolin RJS. Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions. Microorganisms 2023; 11:1668. [PMID: 37512841 PMCID: PMC10386303 DOI: 10.3390/microorganisms11071668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.
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Affiliation(s)
- Bianca C F Santiago
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Iara D de Souza
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - João Vitor F Cavalcante
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Diego A A Morais
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
| | - Mikaelly B da Silva
- Food Engineering Department, Federal University of Campina Grande, Campina Grande 58401-490, Brazil
| | | | - Rodrigo J S Dalmolin
- Bioinformatics Multidisciplinary Environment-IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil
- Department of Biochemistry-CB, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil
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12
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El-Liethy MA, Hemdan BA, El-Taweel GE. New insights for tracking bacterial community structures in industrial wastewater from textile factories to surface water using phenotypic, 16S rRNA isolates identifications and high-throughput sequencing. Acta Trop 2023; 238:106806. [PMID: 36574894 DOI: 10.1016/j.actatropica.2022.106806] [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: 08/18/2022] [Revised: 11/13/2022] [Accepted: 12/24/2022] [Indexed: 12/26/2022]
Abstract
Industrial wastewater can possibly change the microbial ecological environment. There are few studies that focus on the bacterial variety in textile wastewater effluents and after combination with domestic wastewater. Thus, this study aimed to determine dye degrading bacteria from textile wastewater and environmental water samples using cultural method followed by phenotypic using BIOLOG and genotypic identification (16S rRNA) for dye degrading isolates identifications. Moreover, the bacterial communities in three textile and four environmental samples using Illumina MiSeq high-throughput sequencing were investigated. The findings revealed that in textile water samples, the ratio of dye-degrading bacteria (DDB) to total bacterial counts (TBC) was 27%. The identified DDB genera by 16S rRNA based on the cultural approach were Citrobacter spp., Klebsiella spp., Enterobacter spp., Pseudomonas spp., and Aeromonas spp. Regarding to the metagenomics analyses, the environmental samples had 5,598 Operational Toxanomic Units (OTUs) more than textile wastewater samples (1,463 OTUs). Additionally, the most abundant phyla in the textile wastewater were Proteobacteria (24.45-94.83%), Bacteriodetes (0.5-44.84%) and Firmicutes (3.72-67.40%), while, Proteobacteria (30.8-76.3%), bacteroidetes (8.5-50%) and Acentobacteria (0.5-23.12%) were the most abundant phyla in the environmental samples. The maximum abundant bacteria at species level in environmental samples were Aquabacterium parvum (36.71%), Delftia tsuruhatensis (17.61%), Parabacteriodes chartae (15.39%) and Methylorubrum populi (7.51%) in El-Rahawy Drain water (RDW), River Nile water (RNW), wastewater (RWW) from WWTP in Zennin and El-Rahawy Drain sediment (RDS), respectively, whereas the maximum abundant bacteria at species level in textile wastewater were Alkalibacterium pelagium (34.11%), Enterobacter kobei (26.09%) and Chryseobacterium montanum (16.93%) in factory 1 (HBT) sample, SHB sample (before mixing with domestic wastewater) and SHB sample (after mixing with domestic wastewater), respectively. In conclusion, the microbial communities in textile wastewaters are similar to those in environmental samples at the phylum level but distinct at the genus and species levels because they are exposed to a wider range of environmental circumstances.
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Affiliation(s)
- Mohamed Azab El-Liethy
- Environmental Microbiology Laboratory, Water Pollution Research Department, National Research Centre, Dokki, Giza 12622, Egypt.
| | - Bahaa A Hemdan
- Environmental Microbiology Laboratory, Water Pollution Research Department, National Research Centre, Dokki, Giza 12622, Egypt
| | - Gamila E El-Taweel
- Environmental Microbiology Laboratory, Water Pollution Research Department, National Research Centre, Dokki, Giza 12622, Egypt
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13
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Lahiri D, Nag M, Dey A, Sarkar T, Pati S, Nirmal NP, Ray RR, Upadhye VJ, Pandit S, Moovendhan M, Kavisri M. Marine bioactive compounds as antibiofilm agent: a metabolomic approach. Arch Microbiol 2023; 205:54. [PMID: 36602609 DOI: 10.1007/s00203-022-03391-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/17/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023]
Abstract
The ocean is a treasure trove of both living and nonliving creatures, harboring incredibly diverse group of organisms. A plethora of marine sourced bioactive compounds are discovered over the past few decades, many of which are found to show antibiofilm activity. These are of immense clinical significance since the formation of microbial biofilm is associated with the development of high antibiotic resistance. Biofilms are also responsible to bring about problems associated with industries. In fact, the toilets and wash-basins also show degradation due to development of biofilm on their surfaces. Antimicrobial resistance exhibited by the biofilm can be a potent threat not only for the health care unit along with industries and daily utilities. Various recent studies have shown that the marine members of various kingdom are capable of producing antibiofilm compounds. Many such compounds are with unique structural features and metabolomics approaches are essential to study such large sets of metabolites. Associating holobiome metabolomics with analysis of their chemical attribute may bring new insights on their antibiofilm effect and their applicability as a substitute for conventional antibiotics. The application of computer-aided drug design/discovery (CADD) techniques including neural network approaches and structured-based virtual screening, ligand-based virtual screening in combination with experimental validation techniques may help in the identification of these molecules and evaluation of their drug like properties.
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Affiliation(s)
- Dibyajit Lahiri
- Department of Biotechnology, University of Engineering & Management, Kolkata, 700160, West Bengal, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering & Management, Kolkata, 700160, West Bengal, India
| | - Ankita Dey
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Government of West Bengal, Malda, 732102, West Bengal, India
| | - Siddhartha Pati
- Nat Nov Bioscience Private Limited, Balasore, 756001, Odisha, India
| | - Nilesh P Nirmal
- Institute of Nutrition, Mahidol University, 999 Phutthamonthon 4 Road, Salaya, 73170, Nakhon Pathom, Thailand.
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India.
| | - Vijay Jagdish Upadhye
- Center of Research for Development (CR4D), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, Gujarat, India
| | - Soumya Pandit
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, 201306, India
| | - M Moovendhan
- Centre for Ocean Research (DST-FIST Sponsored Centre) MoES-Earth Science & Technology Cell, Col. Dr. Jeppiaar Research Park, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamil Nadu, India
| | - M Kavisri
- Department of Civil Engineering, School of Building and Environment, Sathyabama Institute of Science and Technology, Chennai, 600119, India
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14
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Contreras MJ, Núñez-Montero K, Bruna P, Zárate A, Pezo F, García M, Leal K, Barrientos L. Mammals' sperm microbiome: current knowledge, challenges, and perspectives on metagenomics of seminal samples. Front Microbiol 2023; 14:1167763. [PMID: 37138598 PMCID: PMC10149849 DOI: 10.3389/fmicb.2023.1167763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Bacterial growth is highly detrimental to sperm quality and functionality. However, during the last few years, using sequencing techniques with a metagenomic approach, it has been possible to deepen the study of bacteria-sperm relationships and describe non-culturable species and synergistic and antagonistic relationships between the different species in mammalian animals. We compile the recent metagenomics studies performed on mammalian semen samples and provide updated evidence to understand the importance of the microbial communities in the results of sperm quality and sperm functionality of males, looking for future perspectives on how these technologies can collaborate in the development of andrological knowledge.
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Affiliation(s)
- María José Contreras
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Kattia Núñez-Montero
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco, Chile
| | - Pablo Bruna
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Ana Zárate
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Felipe Pezo
- Escuela de Medicina Veterinaria, Facultad de Recursos Naturales y Medicina Veterinaria, Universidad Santo Tomás, Santiago, Chile
| | - Matías García
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Karla Leal
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- *Correspondence: Leticia Barrientos,
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15
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Abstract
Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.
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16
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Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.
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Affiliation(s)
- Pedro Escudeiro
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Christopher S. Henry
- Argonne National Laboratory, Lemont, Illinois, USA,University of Chicago, Chicago, Illinois, USA
| | - Ricardo P.M. Dias
- BioISI - Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,iXLab - Innovation for National Biological Resilience, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal,Corresponding author.
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17
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Yow HY, Govindaraju K, Lim AH, Abdul Rahim N. Optimizing Antimicrobial Therapy by Integrating Multi-Omics With Pharmacokinetic/Pharmacodynamic Models and Precision Dosing. Front Pharmacol 2022; 13:915355. [PMID: 35814236 PMCID: PMC9260690 DOI: 10.3389/fphar.2022.915355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 12/02/2022] Open
Abstract
In the era of “Bad Bugs, No Drugs,” optimizing antibiotic therapy against multi-drug resistant (MDR) pathogens is crucial. Mathematical modelling has been employed to further optimize dosing regimens. These models include mechanism-based PK/PD models, systems-based models, quantitative systems pharmacology (QSP) and population PK models. Quantitative systems pharmacology has significant potential in precision antimicrobial chemotherapy in the clinic. Population PK models have been employed in model-informed precision dosing (MIPD). Several antibiotics require close monitoring and dose adjustments in order to ensure optimal outcomes in patients with infectious diseases. Success or failure of antibiotic therapy is dependent on the patient, antibiotic and bacterium. For some drugs, treatment responses vary greatly between individuals due to genotype and disease characteristics. Thus, for these drugs, tailored dosing is required for successful therapy. With antibiotics, inappropriate dosing such as insufficient dosing may put patients at risk of therapeutic failure which could lead to mortality. Conversely, doses that are too high could lead to toxicities. Hence, precision dosing which customizes doses to individual patients is crucial for antibiotics especially those with a narrow therapeutic index. In this review, we discuss the various strategies in optimizing antimicrobial therapy to address the challenges in the management of infectious diseases and delivering personalized therapy.
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Affiliation(s)
- Hui-Yin Yow
- Faculty of Health and Medical Sciences, School of Pharmacy, Taylor’s University, Subang Jaya, Malaysia
- Centre for Drug Discovery and Molecular Pharmacology, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya, Malaysia
| | - Kayatri Govindaraju
- Department of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Audrey Huili Lim
- Centre for Clinical Outcome Research (CCORE), Institute for Clinical Research, National Institutes of Health, Shah Alam, Malaysia
| | - Nusaibah Abdul Rahim
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Nusaibah Abdul Rahim,
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18
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Andrade-Martínez JS, Camelo Valera LC, Chica Cárdenas LA, Forero-Junco L, López-Leal G, Moreno-Gallego JL, Rangel-Pineros G, Reyes A. Computational Tools for the Analysis of Uncultivated Phage Genomes. Microbiol Mol Biol Rev 2022; 86:e0000421. [PMID: 35311574 PMCID: PMC9199400 DOI: 10.1128/mmbr.00004-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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Affiliation(s)
- Juan Sebastián Andrade-Martínez
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Carolina Camelo Valera
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Luis Alberto Chica Cárdenas
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Laura Forero-Junco
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | - Gamaliel López-Leal
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - J. Leonardo Moreno-Gallego
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Guillermo Rangel-Pineros
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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19
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OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
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20
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Recent Advances in Biological Recycling of Polyethylene Terephthalate (PET) Plastic Wastes. Bioengineering (Basel) 2022; 9:bioengineering9030098. [PMID: 35324787 PMCID: PMC8945055 DOI: 10.3390/bioengineering9030098] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Polyethylene terephthalate (PET) is one of the most commonly used polyester plastics worldwide but is extremely difficult to be hydrolyzed in a natural environment. PET plastic is an inexpensive, lightweight, and durable material, which can readily be molded into an assortment of products that are used in a broad range of applications. Most PET is used for single-use packaging materials, such as disposable consumer items and packaging. Although PET plastics are a valuable resource in many aspects, the proliferation of plastic products in the last several decades have resulted in a negative environmental footprint. The long-term risk of released PET waste in the environment poses a serious threat to ecosystems, food safety, and even human health in modern society. Recycling is one of the most important actions currently available to reduce these impacts. Current clean-up strategies have attempted to alleviate the adverse impacts of PET pollution but are unable to compete with the increasing quantities of PET waste exposed to the environment. In this review paper, current PET recycling methods to improve life cycle and waste management are discussed, which can be further implemented to reduce plastics pollution and its impacts on health and environment. Compared with conventional mechanical and chemical recycling processes, the biotechnological recycling of PET involves enzymatic degradation of the waste PET and the followed bioconversion of degraded PET monomers into value-added chemicals. This approach creates a circular PET economy by recycling waste PET or upcycling it into more valuable products with minimal environmental footprint.
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21
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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22
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Vuong P, Wise MJ, Whiteley AS, Kaur P. Small investments with big returns: environmental genomic bioprospecting of microbial life. Crit Rev Microbiol 2022; 48:641-655. [PMID: 35100064 DOI: 10.1080/1040841x.2021.2011833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms and their natural products are major drivers of ecological processes and industrial applications. Microbial bioprospecting has been critical for the advancement in various fields such as pharmaceuticals, sustainable industries, food security and bioremediation. Next generation sequencing has been paramount in the exploration of diverse environmental microbiomes. It presents a culture-independent approach to investigating hitherto uncultured taxa, resulting in the creation of massive sequence databases, which are available in the public domain. Genome mining searches available (meta)genomic data for target biosynthetic genes, and combined with the large-scale public data, this in-silico bioprospecting method presents an efficient and extensive way to uncover microbial bioproducts. Bioinformatic tools have progressed to a stage where we can recover genomes from the environment; these metagenome-assembled genomes present a way to understand the metabolic capacity of microorganisms in a physiological and ecological context. Environmental sampling been extensive across various ecological settings, including microbiomes with unique physicochemical properties that could influence the discovery of novel functions and metabolic pathways. Although in-silico methods cannot completely substitute in-vitro studies, the contextual information it provides is invaluable for understanding the ecological and taxonomic distribution of microbial genotypes and to form effective strategies for future microbial bioprospecting efforts.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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Behera SS, Ray RC. Bioprospecting of cowdung microflora for sustainable agricultural, biotechnological and environmental applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100018. [PMID: 34841310 PMCID: PMC8610318 DOI: 10.1016/j.crmicr.2020.100018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/28/2022] Open
Abstract
The review aims at highlighting the manifold applications of cow dung (CD) and CD microflora covering agricultural, biotechnological and environmental applications. The update research on CD microflora and CD in agricultural domain such as biocontrol, growth promotion, organic fertilizer, sulfur oxidation, phosphorus solubilization, zinc mobilization and underlying mechanisms involved in these processes are discussed. The significance of CD applications in tropical agriculture in context to climate change is briefly emphasized. The advances on genomics and proteomics of CD microflora for enhanced yield of enzymes, organic acids, alternative fuels (biomethane and biohydrogen) and other biocommodities, and environmental applications in context to biosorption of heavy metals, biodegradation of xenobiotics, etc. have been given critical attention.
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Key Words
- AD, anaerobic digesters
- AP, apple pomace
- ARB, antibiotic-resistant bacteria
- ARGs, antibiotic-resistant genes
- BOD, biochemical oxygen demand
- Biocontrol
- Biodegradation
- Biogas
- Bioprocess
- Bioremediation
- Biosorption
- C/N, carbon nitrogen ratio
- CD, cow dung
- CDP, cow dung powder
- CEC, cation exchange capacity
- Cow dung
- DO, dissolved oxygen
- EC, electric conductivity
- IAA, indole-3-acetic acids
- NPK, nitrogen, phosphorus, and potassium
- NPP, net primary productivity
- OM, organic matter
- PGPR, plant growth promoting rhizobateria
- PSM, P-solubilizing microorganisms
- Panchagavya
- SGR, specific growth rate
- SSF, solid sate fermentation
- SmF, sub-merged fermentation
- TOC, total organic carbon
- TPPB, two phase partitioning bioreactor
- TS, total solids
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Affiliation(s)
- Sudhanshu S Behera
- Department of Biotechnology, National Institute of Technology, GE Road, Raipur 492010, India.,Department of Fisheries and Animal Resource Development, Government of Odisha, India
| | - Ramesh C Ray
- Centre for Food Biology and Environment Studies, Bhubaneswar 751019, India
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Cho SY, Choi JH, Lee SH, Choi YS, Hwang SW, Kim YJ. Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes. PLoS One 2021; 16:e0259596. [PMID: 34739518 PMCID: PMC8570478 DOI: 10.1371/journal.pone.0259596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/21/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Although the study of respiratory microbiota has been an active field of research, obtaining the appropriate respiratory samples for healthy controls remains to be a challenge. As such, this study aims to evaluate the use of endotracheal tube washing as a viable control for sputum samples. METHODS A total of 14 subjects, including 8 healthy respiratory controls and 6 diabetic patients without any respiratory disease, were enrolled in this study, during which the endotracheal tubes used in their scheduled routine surgery were collected. Pre-operative oral gargles were also collected from non-diabetic subjects. RESULTS 16S amplicon sequencing revealed similar taxa composition in endotracheal tube washings and oral gargles in the healthy control subjects, although the relative abundance of 11 genus level operational taxonomic units was significantly different between the two sample sources. The diabetic subjects showed relatively lower diversity than those of non-diabetic subjects. The proportion range of the most abundant taxa detected in each endotracheal tube washings were 10.1-33.2%. CONCLUSION Endotracheal tube washing fluid may provide healthy control samples for upper respiratory investigations without incurring any additional risk to the subject.
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Affiliation(s)
- Sun Young Cho
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Jeong-Hyun Choi
- Department of Anesthesiology, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Seung Hyeun Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Yong-Sung Choi
- Department of Pediatrics, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Sung Wook Hwang
- Department of Anesthesiology and Pain Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
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Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches. Microbiol Spectr 2021; 9:e0067821. [PMID: 34668733 PMCID: PMC8528112 DOI: 10.1128/spectrum.00678-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Rhizosphere and root-associated bacteria are key components of crop production and sustainable agriculture. However, utilization of these beneficial bacteria is often limited by conventional culture techniques because a majority of soil microorganisms cannot be cultured using standard laboratory media. Therefore, the purpose of this study was to improve culturability and investigate the diversity of the bacterial communities from the wheat rhizosphere microbiome collected from three locations in Egypt with contrasting soil characteristics by using metagenomic analysis and improved culture-based methods. The improved strategies of the culture-dependent approach included replacing the agar in the medium with gellan gums and modifying its preparation by autoclaving the phosphate and gelling agents separately. Compared to the total operational taxonomic units (OTUs) observed from the metagenomic data sets derived from the three analyzed soils, 1.86 to 2.52% of the bacteria were recovered using the modified cultivation strategies, whereas less than 1% were obtained employing the standard cultivation protocols. Twenty-one percent of the cultivable isolates exhibited multiple plant growth-promoting (PGP) properties, including P solubilization activity and siderophore production. From the metagenomic analysis, the most abundant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, and Firmicutes. Moreover, the relative abundance of the specific bacterial taxa was correlated with the soil characteristics, demonstrating the effect of the soil in modulating the plant rhizosphere microbiome. IMPORTANCE Bacteria colonizing the rhizosphere, a narrow zone of soil surrounding the root system, are known to have beneficial effects in improving the growth and stress tolerance of plants. However, most bacteria in natural environments, especially those in rhizosphere soils, are recalcitrant to cultivation using traditional techniques, and thus their roles in soil health and plant growth remain unexplored. Hence, investigating new culture media and culture conditions to bring “not-yet-cultured” species into cultivation and to identify new functions is still an important task for all microbiologists. To this end, we describe improved cultivation protocols that increase the number and diversity of cultured bacteria from the rhizosphere of wheat plants. Using such approaches will lead to new insights into culturing more beneficial bacteria that live in the plant rhizosphere, in so doing creating greater opportunities not only for field application but also for promoting sustainability.
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26
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Metagenomic analysis of microbial communities in the sediments of a semi-intensive penaeid shrimp culture system. J Genet Eng Biotechnol 2021; 19:136. [PMID: 34499256 PMCID: PMC8429531 DOI: 10.1186/s43141-021-00237-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/29/2021] [Indexed: 11/30/2022]
Abstract
The present study reports metagenomic sequencing and microbial diversity analysis of the sediment samples of a semi-intensive penaeid shrimp culture system. 16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities in the analyzed sample. Analysis of the results showed a high abundance of Proteobacteria followed by Verrucomicrobia, Bacteroidetes, Planctomycetes, Firmicutes, Cyanobacteria, and Actinobacteria in the metagenome retrieved from the sediment sample. Unclassified bacteria also contributed a significant portion of the metagenome. Two potential shrimp pathogens viz Vibrio harveyi and Acinetobacter lwoffii detected in the sediment sample show the risk associated with the pond. Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. The present study provides preliminary data with respect to the microbial community present in the sediments of a shrimp culture system and emphasizes the application of metagenomics in exploring the microbial diversity of aquaculture systems, which might help in the early detection of pathogens within the system and helps to develop pathogen control strategies in semi-intensive aquaculture systems.
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27
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Microbial communities associated with the ostracods Candona sp. inhabiting the area of the methane seep Goloustnoye (Lake Baikal). Symbiosis 2021. [DOI: 10.1007/s13199-021-00802-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Gaio D, DeMaere MZ, Anantanawat K, Chapman TA, Djordjevic SP, Darling AE. Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes. Microb Genom 2021; 7. [PMID: 34370660 PMCID: PMC8549361 DOI: 10.1099/mgen.0.000501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Using a previously described metagenomics dataset of 27 billion reads, we reconstructed over 50 000 metagenome-assembled genomes (MAGs) of organisms resident in the porcine gut, 46.5 % of which were classified as >70 % complete with a <10 % contamination rate, and 24.4 % were nearly complete genomes. Here, we describe the generation and analysis of those MAGs using time-series samples. The gut microbial communities of piglets appear to follow a highly structured developmental programme in the weeks following weaning, and this development is robust to treatments including an intramuscular antibiotic treatment and two probiotic treatments. The high resolution we obtained allowed us to identify specific taxonomic ‘signatures’ that characterize the gut microbial development immediately after weaning. Additionally, we characterized the carbohydrate repertoire of the organisms resident in the porcine gut. We tracked the abundance shifts of 294 carbohydrate active enzymes, and identified the species and higher-level taxonomic groups carrying each of these enzymes in their MAGs. This knowledge can contribute to the design of probiotics and prebiotic interventions as a means to modify the piglet gut microbiome.
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Affiliation(s)
- Daniela Gaio
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Matthew Z DeMaere
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Kay Anantanawat
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Aaron E Darling
- iThree Institute, University of Technology Sydney, Sydney, New South Wales, Australia
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29
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Diwan AD, Harke SN, Gopalkrishna, Panche AN. Aquaculture industry prospective from gut microbiome of fish and shellfish: An overview. J Anim Physiol Anim Nutr (Berl) 2021; 106:441-469. [PMID: 34355428 DOI: 10.1111/jpn.13619] [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: 05/08/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 12/17/2022]
Abstract
The microbiome actually deals with micro-organisms that are associated with indigenous body parts and the entire gut system in all animals, including human beings. These microbes are linked with roles involving hereditary traits, defence against diseases and strengthening overall immunity, which determines the health status of an organism. Considerable efforts have been made to find out the microbiome diversity and their taxonomic identification in finfish and shellfish and its importance has been correlated with various physiological functions and activities. In recent past due to the availability of advanced molecular tools, some efforts have also been made on DNA sequencing of these microbes to understand the environmental impact and other stress factors on their genomic structural profile. There are reports on the use of next-generation sequencing (NGS) technology, including amplicon and shot-gun approaches, and associated bioinformatics tools to count and classify commensal microbiome at the species level. The microbiome present in the whole body, particularly in the gut systems of finfish and shellfish, not only contributes to digestion but also has an impact on nutrition, growth, reproduction, immune system and vulnerability of the host fish to diseases. Therefore, the study of such microbial communities is highly relevant for the development of new and innovative bio-products which will be a vital source to build bio and pharmaceutical industries, including aquaculture. In recent years, attempts have been made to discover the chemical ingredients present in these microbes in the form of biomolecules/bioactive compounds with their functions and usefulness for various health benefits, particularly for the treatment of different types of disorders in animals. Therefore, it has been speculated that microbiomes hold great promise not only as a cure for ailments but also as a preventive measure for the number of infectious diseases. This kind of exploration of new breeds of microbes with their miraculous ingredients will definitely help to accelerate the development of the drugs, pharmaceutical and other biological related industries. Probiotic research and bioinformatics skills will further escalate these opportunities in the sector. In the present review, efforts have been made to collect comprehensive information on the finfish and shellfish microbiome, their diversity and functional properties, relationship with diseases, health status, data on species-specific metagenomics, probiotic research and bioinformatics skills. Further, emphasis has also been made to carry out microbiome research on priority basis not only to keep healthy environment of the fish farming sector but also for the sustainable growth of biological related industries, including aquaculture.
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Affiliation(s)
- Arvind D Diwan
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Sanjay N Harke
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
| | - Gopalkrishna
- Central Institute of Fisheries Education (CIFE, Deemed University), ICAR, Mumbai, India
| | - Archana N Panche
- Mahatma Gandhi Mission's (MGM) Institute of Biosciences and Technology, MGM University, Aurangabad, Maharashtra, India
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Abstract
The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Toni Gabaldón
- Barcelona Supercomputing Centre (BCS-CNS), 08034 Barcelona, Spain; .,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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31
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The Root Microbiome of Salicornia ramosissima as a Seedbank for Plant-Growth Promoting Halotolerant Bacteria. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Root−associated microbial communities play important roles in the process of adaptation of plant hosts to environment stressors, and in this perspective, the microbiome of halophytes represents a valuable model for understanding the contribution of microorganisms to plant tolerance to salt. Although considered as the most promising halophyte candidate to crop cultivation, Salicornia ramosissima is one of the least-studied species in terms of microbiome composition and the effect of sediment properties on the diversity of plant-growth promoting bacteria associated with the roots. In this work, we aimed at isolating and characterizing halotolerant bacteria associated with the rhizosphere and root tissues of S. ramosissima, envisaging their application in saline agriculture. Endophytic and rhizosphere bacteria were isolated from wild and crop cultivated plants, growing in different estuarine conditions. Isolates were identified based on 16S rRNA sequences and screened for plant-growth promotion traits. The subsets of isolates from different sampling sites were very different in terms of composition but consistent in terms of the plant-growth promoting traits represented. Bacillus was the most represented genus and expressed the wider range of extracellular enzymatic activities. Halotolerant strains of Salinicola, Pseudomonas, Oceanobacillus, Halomonas, Providencia, Bacillus, Psychrobacter and Brevibacterium also exhibited several plant-growth promotion traits (e.g., 3-indole acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophores, phosphate solubilization). Considering the taxonomic diversity and the plant-growth promotion potential of the isolates, the collection represents a valuable resource that can be used to optimize the crop cultivation of Salicornia under different environmental conditions and for the attenuation of salt stress in non-halophytes, considering the global threat of arable soil salinization.
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32
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González-Cabaleiro R, Martinez-Rabert E, Argiz L, van Kessel MA, Smith CJ. A framework based on fundamental biochemical principles to engineer microbial community dynamics. Curr Opin Biotechnol 2021; 67:111-118. [PMID: 33540361 DOI: 10.1016/j.copbio.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
Microbial communities are complex but there are basic principles we can apply to constrain the assumed stochasticity of their activity. By understanding the trade-offs behind the kinetic parameters that define microbial growth, we can explain how local interspecies dependencies arise and shape the emerging properties of a community. If we integrate these theoretical descriptions with experimental 'omics' data and bioenergetics analysis of specific environmental conditions, predictions on activity, assembly and spatial structure can be obtained reducing the a priori unpredictable complexity of microbial communities. This information can be used to define the appropriate selective pressures to engineer bioprocesses and propose new hypotheses which can drive experimental research to accelerate innovation in biotechnology.
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Affiliation(s)
- Rebeca González-Cabaleiro
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK.
| | - Eloi Martinez-Rabert
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
| | - Lucia Argiz
- CRETUS Institute, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - Maartje Ahj van Kessel
- Radboud University, Department of Microbiology, Institute of Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cindy J Smith
- James Watt School of Engineering, Infrastructure and Environment Research Division, University of Glasgow, Rankine Building, Glasgow, G12 8LT, UK
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BenIsrael M, Habtewold JZ, Khosla K, Wanner P, Aravena R, Parker BL, Haack EA, Tsao DT, Dunfield KE. Identification of degrader bacteria and fungi enriched in rhizosphere soil from a toluene phytoremediation site using DNA stable isotope probing. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2021; 23:846-856. [PMID: 33397125 DOI: 10.1080/15226514.2020.1860901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Improved knowledge of the ecology of contaminant-degrading organisms is paramount for effective assessment and remediation of aromatic hydrocarbon-impacted sites. DNA stable isotope probing was used herein to identify autochthonous degraders in rhizosphere soil from a hybrid poplar phytoremediation system incubated under semi-field-simulated conditions. High-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer (ITS) rRNA genes in metagenomic samples separated according to nucleic acid buoyant density was used to identify putative toluene degraders. Degrader bacteria were found mainly within the Actinobacteria and Proteobacteria phyla and classified predominantly as Cupriavidus, Rhodococcus, Luteimonas, Burkholderiaceae, Azoarcus, Cellulomonadaceae, and Pseudomonas organisms. Purpureocillium lilacinum and Mortierella alpina fungi were also found to assimilate toluene, while several strains of the fungal poplar endophyte Mortierella elongatus were indirectly implicated as potential degraders. Finally, PICRUSt2 predictive taxonomic functional modeling of 16S rRNA genes was performed to validate successful isolation of stable isotope-labeled DNA in density-resolved samples. Four unique sequences, classified within the Bdellovibrionaceae, Intrasporangiaceae, or Chitinophagaceae families, or within the Sphingobacteriales order were absent from PICRUSt2-generated models and represent potentially novel putative toluene-degrading species. This study illustrates the power of combining stable isotope amendment with advanced metagenomic and bioinformatic techniques to link biodegradation activity with unisolated microorganisms. Novelty statement: This study used emerging molecular biological techniques to identify known and new organisms implicated in aromatic hydrocarbon biodegradation from a field-scale phytoremediation system, including organisms with phyto-specific relevance and having potential for downstream applications (amendment or monitoring) in future and existing systems. Additional novelty in this study comes from the use of taxonomic functional modeling approaches for validation of stable isotope probing techniques. This study provides a basis for expanding existing reference databases of known aromatic hydrocarbon degraders from field-applicable sources and offers technological improvements for future site assessment and management purposes.
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Affiliation(s)
- Michael BenIsrael
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | | | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Philipp Wanner
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
| | - Ramon Aravena
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
- Department of Earth and Environmental Sciences, University of Waterloo, Waterloo, Canada
| | - Beth L Parker
- G360 Institute for Groundwater Research, University of Guelph, Guelph, Canada
| | | | - David T Tsao
- BP Corporation North America, Inc, Naperville, IL, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Canada
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Utermann C, Echelmeyer VA, Oppong-Danquah E, Blümel M, Tasdemir D. Diversity, Bioactivity Profiling and Untargeted Metabolomics of the Cultivable Gut Microbiota of Ciona intestinalis. Mar Drugs 2020; 19:6. [PMID: 33374243 PMCID: PMC7824411 DOI: 10.3390/md19010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/13/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
It is widely accepted that the commensal gut microbiota contributes to the health and well-being of its host. The solitary tunicate Ciona intestinalis emerges as a model organism for studying host-microbe interactions taking place in the gut, however, the potential of its gut-associated microbiota for marine biodiscovery remains unexploited. In this study, we set out to investigate the diversity, chemical space, and pharmacological potential of the gut-associated microbiota of C. intestinalis collected from the Baltic and North Seas. In a culture-based approach, we isolated 61 bacterial and 40 fungal strains affiliated to 33 different microbial genera, indicating a rich and diverse gut microbiota dominated by Gammaproteobacteria. In vitro screening of the crude microbial extracts indicated their antibacterial (64% of extracts), anticancer (22%), and/or antifungal (11%) potential. Nine microbial crude extracts were prioritized for in-depth metabolome mining by a bioactivity- and chemical diversity-based selection procedure. UPLC-MS/MS-based metabolomics combining automated (feature-based molecular networking and in silico dereplication) and manual approaches significantly improved the annotation rates. A high chemical diversity was detected where peptides and polyketides were the predominant classes. Many compounds remained unknown, including two putatively novel lipopeptides produced by a Trichoderma sp. strain. This is the first study assessing the chemical and pharmacological profile of the cultivable gut microbiota of C. intestinalis.
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Affiliation(s)
- Caroline Utermann
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (C.U.); (V.A.E.); (E.O.-D.); (M.B.)
| | - Vivien A. Echelmeyer
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (C.U.); (V.A.E.); (E.O.-D.); (M.B.)
| | - Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (C.U.); (V.A.E.); (E.O.-D.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (C.U.); (V.A.E.); (E.O.-D.); (M.B.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (C.U.); (V.A.E.); (E.O.-D.); (M.B.)
- Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
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35
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Genitsaris S, Stefanidou N, Leontidou K, Matsi T, Karamanoli K, Mellidou I. Bacterial Communities in the Rhizosphere and Phyllosphere of Halophytes and Drought-Tolerant Plants in Mediterranean Ecosystems. Microorganisms 2020; 8:E1708. [PMID: 33142812 PMCID: PMC7692439 DOI: 10.3390/microorganisms8111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of the study was to investigate the bacterial community diversity and structure by means of 16S rRNA gene high-throughput amplicon sequencing, in the rhizosphere and phyllosphere of halophytes and drought-tolerant plants in Mediterranean ecosystems with different soil properties. The locations of the sampled plants included alkaline, saline-sodic soils, acidic soils, and the volcanic soils of Santorini Island, differing in soil fertility. Our results showed high bacterial richness overall with Proteobacteria and Actinobacteria dominating in terms of OTUs number and indicated that variable bacterial communities differed depending on the plant's compartment (rhizosphere and phyllosphere), the soil properties and location of sampling. Furthermore, a shared pool of generalist bacterial taxa was detected independently of sampling location, plant species, or plant compartment. We conclude that the rhizosphere and phyllosphere of native plants in stressed Mediterranean ecosystems consist of common bacterial assemblages contributing to the survival of the plant, while at the same time the discrete soil properties and environmental pressures of each habitat drive the development of a complementary bacterial community with a distinct structure for each plant and location. We suggest that this trade-off between generalist and specialist bacterial community is tailored to benefit the symbiosis with the plant.
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Affiliation(s)
- Savvas Genitsaris
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Kleopatra Leontidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Laboratory of Agricultural Chemistry, School of Agriculture, Aristotle University of Thessaloniki, 54 124 Thessaloniki, Greece
- Institute of Plant Breeding and Genetic Resources, HAO ELGO-DEMETER, 57 001 Thermi, Greece
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Houghton KM, Stewart LC. Temperature-gradient incubation isolates multiple competitive species from a single environmental sample. Access Microbiol 2020; 2:acmi000081. [PMID: 32974564 PMCID: PMC7470311 DOI: 10.1099/acmi.0.000081] [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: 10/13/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
High-throughput sequencing has allowed culture-independent investigation into a wide variety of microbiomes, but sequencing studies still require axenic culture experiments to determine ecological roles, confirm functional predictions and identify useful compounds and pathways. We have developed a new method for culturing and isolating multiple microbial species with overlapping ecological niches from a single environmental sample, using temperature-gradient incubation. This method was more effective than standard serial dilution-to-extinction at isolating methanotrophic bacteria. It also highlighted discrepancies between culture-dependent and -independent techniques; 16S rRNA gene amplicon sequencing of the same sample did not accurately reflect cultivatable strains using this method. We propose that temperature-gradient incubation could be used to separate out and study previously ‘unculturable’ strains, which co-exist in both natural and artificial environments.
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Affiliation(s)
- Karen M Houghton
- GNS Science, Wairakei Research Centre, 114 Karetoto Rd, Taupō 3384, New Zealand
| | - Lucy C Stewart
- GNS Science, 1 Fairway Drive, Avalon, Lower Hutt 5010, New Zealand
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Yukgehnaish K, Kumar P, Sivachandran P, Marimuthu K, Arshad A, Paray BA, Arockiaraj J. Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish. REVIEWS IN AQUACULTURE 2020; 12:1903-1927. [DOI: 10.1111/raq.12416] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/03/2020] [Indexed: 10/16/2023]
Abstract
AbstractFish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial‐resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review.
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Affiliation(s)
| | - Praveen Kumar
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Parimannan Sivachandran
- Faculty of Applied Sciences Centre of Excellence for Omics-Driven Computational Biodiscovery (CO MBio) AIMST University Bedong Malaysia
- Faculty of Science School of Life and Environmental Sciences Engineering and Built Environment Deakin University, Waurn Ponds Campus Geelong Australia
| | - Kasi Marimuthu
- Department of Biotechnology AIMST University Semeling Kedah Darul Aman Malaysia
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS) Universiti Putra Malaysia Serdang Negeri Sembilan Malaysia
- Department of Aquaculture Faculty of Agriculture Universiti Putra Malaysia Serdang Selangor Malaysia
- Laboratory of Marine Biotechnology Institute of Bioscience Universiti Putra Malaysia Serdang Selangor Darul Ehsan Malaysia
| | - Bilal Ahmad Paray
- Department of Zoology College of Science King Saud University Riyadh Saudi Arabia
| | - Jesu Arockiaraj
- SRM Research Institute SRM Institute of Science and Technology Chennai Tamil Nadu India
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Bajinka O, Tan Y, Abdelhalim KA, Özdemir G, Qiu X. Extrinsic factors influencing gut microbes, the immediate consequences and restoring eubiosis. AMB Express 2020; 10:130. [PMID: 32710186 PMCID: PMC7381537 DOI: 10.1186/s13568-020-01066-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
From the emerging studies, the more diverse the microbial population in the gut, the healthier the gut. Health benefits are associated with the functional characteristics of these diverse microbial genes. Extrinsic factors causing dysbiosis are extensively studied however, linking the varying degree of consequences to the respective factors and therapeutic possibilities are not explored at length. This review aims to examine from previous studies and put forward the types of dysbiosis, the immediate consequences and the scientific approaches to restore disrupted microbiota. Dietary supplements are found to be one of the factors contributing profoundly to the alteration of gut microbiota. While diet rich in fibre and fermented food established a diverse microbiome and produce vital metabolites, high fat, animal proteins and high caloric carbohydrate are as well relative to dysbiosis among infants, adult or diseases individuals. The intermittent fasting, feeding methods, the pH and water quality are among the factors associated with dysbiosis. Prebiotics and Probiotics maintain and restore gut homeostasis. Antibiotic-induced dysbiosis are relatively on the spectrum of activity, the pharmacokinetics properties, the dose taken during the treatment route of administration and the duration of drug therapy. The higher the altitude, the lesser the diversity. Extreme temperatures as well are related to reduced microbial activity and metabolism. Delivery through caserium-section deprived the newborn from restoring valuable vaginal bacterial species and the baby will instead assumed intestinal microbiota-like. While exercise and oxidative stress contribute even though moderately, fecal microbial transfer (FMT) also influence gut microbiota.
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Williams AN, Stavrinides J. A Microbial Sampling and Community Reconstruction Activity for Introducing Students to the Burgeoning Field of Metagenomics. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2020; 21:jmbe-21-37. [PMID: 32431770 PMCID: PMC7198221 DOI: 10.1128/jmbe.v21i1.1891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/27/2020] [Indexed: 06/11/2023]
Affiliation(s)
| | - John Stavrinides
- Corresponding author. Mailing address: Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada. Phone: 306-337-8478. E-mail:
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BenIsrael M, Wanner P, Fernandes J, Burken JG, Aravena R, Parker BL, Haack EA, Tsao DT, Dunfield KE. Quantification of toluene phytoextraction rates and microbial biodegradation functional profiles at a fractured bedrock phytoremediation site. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 707:135890. [PMID: 31865073 DOI: 10.1016/j.scitotenv.2019.135890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 05/28/2023]
Abstract
This field study evaluated the efficacy of a mature hybrid poplar phytoremediation system for the remediation of toluene in a fractured bedrock aquifer site. Phytoextraction activity of the trees and the ecology and biodegradation potential of root-colonizing bacteria that ultimately influence how much toluene is transported from the roots and phytoextracted to the aboveground point of measurement were explored. Peak-season toluene mass removal rates ranging from 313 to 743 μg/day were quantified using passive in planta contaminant sampling techniques and continuous heat dissipation transpiration measurements in tree stems. Root bacterial microbiome structure and biodegradation potential were evaluated via high-throughput sequencing and predictive metagenomic functional modelling of bacterial 16S rRNA genes in roots. Poplar roots were colonized mostly by Proteobacteria, Actinobacteria, and Bacteroidetes. Distinct, more uniform communities were observed in roots associated with trees planted in the toluene source area compared to other areas, with differences apparent at lower taxonomic levels. Significant enrichment of Streptomyces in roots was observed in the source area, implicating that genus as a potentially important poplar endophyte at toluene-impacted sites. Moreover, significantly greater aerobic toluene biodegradation capacity was predicted in these roots compared to other areas using taxonomic functional modelling. Together with passive sampling, the molecular results provided supporting evidence of biodegradation activity in the source area and contextualized the detected phytoextraction patterns. These results support the application of phytoremediation systems for aromatic hydrocarbons in environments with complex geology and demonstrate field-validated monitoring techniques to assess phytoextraction and biodegradation in these systems.
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Affiliation(s)
- Michael BenIsrael
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Philipp Wanner
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Jeremy Fernandes
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Joel G Burken
- Civil, Architectural and Environmental Engineering, Missouri University of Science and Technology, 1401 N. Pine St., Rolla, MO 65409-0030, USA
| | - Ramon Aravena
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Beth L Parker
- G(360) Institute for Groundwater Research, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Elizabeth A Haack
- EcoMetrix Inc., 6800 Campobello Road, Mississauga, ON L5N 2L8, Canada
| | - David T Tsao
- BP Corporation North America Inc., 150 W Warrenville Road #605-2E, Naperville, IL 60563, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada.
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Mohammad HA, Madi NM, Al-Nakib W. Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach. Virol J 2020; 17:10. [PMID: 32000795 PMCID: PMC6993487 DOI: 10.1186/s12985-020-1287-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022] Open
Abstract
Background Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.
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Affiliation(s)
- Hawraa Adel Mohammad
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
| | - Nada Mohammed Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait.
| | - Widad Al-Nakib
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
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Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample. Int Microbiol 2020; 23:467-474. [PMID: 31933014 DOI: 10.1007/s10123-020-00119-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/03/2019] [Accepted: 01/07/2020] [Indexed: 10/25/2022]
Abstract
Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.
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Romano I, Ventorino V, Pepe O. Effectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence. FRONTIERS IN PLANT SCIENCE 2020; 11:6. [PMID: 32076431 PMCID: PMC7006617 DOI: 10.3389/fpls.2020.00006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
Issues concerning the use of harmful chemical fertilizers and pesticides that have large negative impacts on environmental and human health have generated increasing interest in the use of beneficial microorganisms for the development of sustainable agri-food systems. A successful microbial inoculant has to colonize the root system, establish a positive interaction and persist in the environment in competition with native microorganisms living in the soil through rhizocompetence traits. Currently, several approaches based on culture-dependent, microscopic and molecular methods have been developed to follow bioinoculants in the soil and plant surface over time. Although culture-dependent methods are commonly used to estimate the persistence of bioinoculants, it is difficult to differentiate inoculated organisms from native populations based on morphological characteristics. Therefore, these methods should be used complementary to culture-independent approaches. Microscopy-based techniques (bright-field, electron and fluorescence microscopy) allow to obtain a picture of microbial colonization outside and inside plant tissues also at high resolution, but it is not possible to always distinguish living cells from dead cells by direct observation as well as distinguish bioinoculants from indigenous microbial populations living in soils. In addition, the development of metagenomic techniques, including the use of DNA probes, PCR-based methods, next-generation sequencing, whole-genome sequencing and pangenome methods, provides a complementary approach useful to understand plant-soil-microbe interactions. However, to ensure good results in microbiological analysis, the first fundamental prerequisite is correct soil sampling and sample preparation for the different methodological approaches that will be assayed. Here, we provide an overview of the advantages and limitations of the currently used methods and new methodological approaches that could be developed to assess the presence, plant colonization and soil persistence of bioinoculants in the rhizosphere. We further discuss the possibility of integrating multidisciplinary approaches to examine the variations in microbial communities after inoculation and to track the inoculated microbial strains.
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Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- *Correspondence: Valeria Ventorino,
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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Armitage GC. A brief history of periodontics in the United States of America: Pioneers and thought-leaders of the past, and current challenges. Periodontol 2000 2019; 82:12-25. [PMID: 31850629 DOI: 10.1111/prd.12303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper summarizes historical events in periodontology in the United States over the past 200 years. The contributions of some of the key thought-leaders of the past are highlighted. Throughout the 20th century, the evolution of thought, leading to the views currently held regarding the pathogenesis and treatment of periodontal diseases, was significantly influenced by: (1) major changes in health-care education; (2) the emergence of periodontics as a specialty of dentistry; (3) the publication of peer-reviewed journals with an emphasis on periodontology; (4) formation of the National Institute of Dental and Craniofacial Research (NIDCR); and (5) expansion of periodontal research programs by the NIDCR. The two major future challenges facing periodontal research are development of a better understanding of the ecological complexities of host-microbial interactions in periodontal health and disease, and identification of the relevant mechanisms involved in the predictable regeneration of damaged periodontal tissues.
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Affiliation(s)
- Gary C Armitage
- Division of Periodontology, Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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Malik YS, Verma AK, Kumar N, Touil N, Karthik K, Tiwari R, Bora DP, Dhama K, Ghosh S, Hemida MG, Abdel-Moneim AS, Bányai K, Vlasova AN, Kobayashi N, Singh RK. Advances in Diagnostic Approaches for Viral Etiologies of Diarrhea: From the Lab to the Field. Front Microbiol 2019; 10:1957. [PMID: 31608017 PMCID: PMC6758846 DOI: 10.3389/fmicb.2019.01957] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/08/2019] [Indexed: 12/25/2022] Open
Abstract
The applications of correct diagnostic approaches play a decisive role in timely containment of infectious diseases spread and mitigation of public health risks. Nevertheless, there is a need to update the diagnostics regularly to capture the new, emergent, and highly divergent viruses. Acute gastroenteritis of viral origin has been identified as a significant cause of mortality across the globe, with the more serious consequences seen at the extremes of age groups (young and elderly) and immune-compromised individuals. Therefore, significant advancements and efforts have been put in the development of enteric virus diagnostics to meet the WHO ASSURED criteria as a benchmark over the years. The Enzyme-Linked Immunosorbent (ELISA) and Polymerase Chain Reaction (PCR) are the basic assays that provided the platform for development of several efficient diagnostics such as real-time RT-PCR, loop-mediated isothermal amplification (LAMP), polymerase spiral reaction (PSR), biosensors, microarrays and next generation sequencing. Herein, we describe and discuss the applications of these advanced technologies in context to enteric virus detection by delineating their features, advantages and limitations.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Atul Kumar Verma
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Naveen Kumar
- ICAR-National Institute of High Security Animal Diseases, OIE Reference Laboratory for Avian Influenza, Bhopal, India
| | - Nadia Touil
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d’Instruction Mohammed V, Rabat, Morocco
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology & Immunology, College of Veterinary Sciences, DUVASU, Mathura, India
| | - Durlav Prasad Bora
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Maged Gomaa Hemida
- Department of Microbiology and Parasitology, College of Veterinary Medicine, King Faisal University, Al-Hufuf, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, Taif, Saudi Arabia
- Department of Virology, Faculty of Veterinary Medicine, Beni Suef University, Beni Suef, Egypt
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anastasia N. Vlasova
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, CFAES, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | | | - Raj Kumar Singh
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, Izatnagar, India
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Hemdan BA, El-Liethy MA, ElMahdy MEI, El-Taweel GE. Metagenomics analysis of bacterial structure communities within natural biofilm. Heliyon 2019; 5:e02271. [PMID: 31485510 PMCID: PMC6716113 DOI: 10.1016/j.heliyon.2019.e02271] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/11/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
The bacterial profiles of natural household biofilm have not been widely investigated. The majorities of these bacterial lineages are not cultivable. Thus, this study aims (i) to enumerate some potential bacterial lineages using culture based method within biofilm samples and confirmed using Biolog GEN III and polymerase chain reaction (PCR). (ii) To investigate the bacterial profiles of communities in two biofilm samples using next generation sequencing (NGS). Forty biofilm samples were cultured and colonies of each selected prevailing potential lineages (E. coli, Salmonella entrica, Pseudomonas aeruginosa, Staphylococcus aureus and Listeria monocytogenes) were selected for confirmation. From obtained results, the counts of the tested bacterial lineages in kitchen biofilm samples were greater than those in bathroom samples. Precision of PCR was higher than Biolog GEN III to confirm the bacterial isolates. Using NGS analysis, the results revealed that a total of 110,554 operational taxonomic units (OTUs) were obtained for two biofilm samples, representing kitchen and bathroom biofilm samples. The numbers of phyla in the kitchen biofilm sample (35 OTUs) was higher than that in bathroom sample (18 OTUs). A total of 435 genera were observed in the bathroom biofilm sample compared to only 256 in the kitchen sample. Evidences have shown that the empirical gadgets for biofilm investigation are becoming convenient and affordable. Many distinct bacterial lineages observed in biofilm are one of the most significant issues that threaten human health and lead to disease outbreaks.
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Affiliation(s)
- Bahaa A Hemdan
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Mohamed Azab El-Liethy
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
| | - M E I ElMahdy
- Environmental Virology Lab., Water Pollution Research Department, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Gamila E El-Taweel
- Environmental Microbiology Lab., Water Pollution Research Department, National Research Centre, Dokki, 12622, Giza, Egypt
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Felz S, Vermeulen P, van Loosdrecht MCM, Lin YM. Chemical characterization methods for the analysis of structural extracellular polymeric substances (EPS). WATER RESEARCH 2019; 157:201-208. [PMID: 30953855 DOI: 10.1016/j.watres.2019.03.068] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Biofilm structure and functionality depend on extracellular polymeric substances (EPS), but analytical methods for EPS often lack specificity which limits progress of biofilm research. EPS were extracted from aerobic granular sludge and analyzed with frequently applied colorimetric methods. The colorimetric methods were evaluated based on their applicability for EPS analysis. EPS fractions of interest were proteins, sugars, uronic acids and phenolic compounds. The applied methods (Lowry method, bicinchoninic acid assay, phenol sulfuric acid method, carbazole sulfuric acid method) were investigated in terms of their sensitivity towards the selected standard compound. Interference of compounds present in EPS with the colorimetric methods was further evaluated. All methods showed to be highly depending on the choice of standard compound and susceptible towards interference by compounds present in EPS. This study shows that currently used colorimetric methods are not capable of accurately characterizing EPS. More advanced methods are needed to be able to draw conclusions about biofilm composition, structure and functionality.
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Affiliation(s)
- Simon Felz
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands.
| | - Pascalle Vermeulen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Yue Mei Lin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
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49
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Garretto A, Hatzopoulos T, Putonti C. virMine: automated detection of viral sequences from complex metagenomic samples. PeerJ 2019; 7:e6695. [PMID: 30993039 PMCID: PMC6462185 DOI: 10.7717/peerj.6695] [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: 11/30/2018] [Accepted: 02/26/2019] [Indexed: 12/29/2022] Open
Abstract
Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.
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Affiliation(s)
- Andrea Garretto
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America
| | - Thomas Hatzopoulos
- Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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50
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Chernov VM, Chernova OA, Mouzykantov AA, Lopukhov LL, Aminov RI. Omics of antimicrobials and antimicrobial resistance. Expert Opin Drug Discov 2019; 14:455-468. [DOI: 10.1080/17460441.2019.1588880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vladislav M. Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Olga A. Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Alexey A. Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russian Federation
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Leonid L. Lopukhov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
| | - Rustam I. Aminov
- Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kazan, Russian Federation
- Applied Health Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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