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Ullah S, Rahman W, Ullah F, Ullah A, Ahmad G, Ijaz M, Ullah H, Sharafmal DM. The HABD: Home of All Biological Databases Empowering Biological Research With Cutting-Edge Database Systems. Curr Protoc 2024; 4:e1063. [PMID: 38808697 DOI: 10.1002/cpz1.1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The emergence of computer technologies and computing power has led to the development of several database systems that provide standardized access to vast quantities of data, making it possible to collect, search, index, evaluate, and extract useful knowledge across various fields. The Home of All Biological Databases (HABD) has been established as a continually expanding platform that aims to store, organize, and distribute biological data in a searchable manner, removing all dead and non-accessible data. The platform meticulously categorizes data into various categories, such as COVID-19 Pandemic Database (CO-19PDB), Database relevant to Human Research (DBHR), Cancer Research Database (CRDB), Latest Database of Protein Research (LDBPR), Fungi Databases Collection (FDBC), and many other databases that are categorized based on biological phenomena. It currently provides a total of 22 databases, including 6 published, 5 submitted, and the remaining in various stages of development. These databases encompass a range of areas, including phytochemical-specific and plastic biodegradation databases. HABD is equipped with search engine optimization (SEO) analyzer and Neil Patel tools, which ensure excellent SEO and high-speed value. With timely updates, HABD aims to facilitate the processing and visualization of data for scientists, providing a one-stop-shop for all biological databases. Computer platforms, such as PhP, html, CSS, Java script and Biopython, are used to build all the databases. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Shahid Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Farhan Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Anees Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Gulzar Ahmad
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Hameed Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
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Dreisbach C, Alhusen J, Prescott S, Dudley D, Trinchieri G, Siega‐Riz AM. Metagenomic characterization of the maternal prenatal gastrointestinal microbiome by pregravid BMI. Obesity (Silver Spring) 2023; 31:412-422. [PMID: 36562201 PMCID: PMC10108029 DOI: 10.1002/oby.23659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/15/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The incidence of women entering into pregnancy with BMI indicating overweight or obesity is rising with concurrent increases in adverse complications such as gestational diabetes. Although several studies have examined the compositional changes to the microbiome across BMI classifications, there has been no investigation regarding changes in microbial function during pregnancy. METHODS A total of 105 gastrointestinal microbiome biospecimens were used in this analysis. Biospecimens were sequenced by using the Illumina NovaSeq 6000 shotgun metagenomics platform. RESULTS Findings indicate an enrichment in microbiota from the phylum Firmicutes across all pregravid BMI groups with a decrease in α diversity in groups with BMI indicating obesity or overweight compared with a group with BMI indicating normal weight (p = 0.02). More specifically, women with BMI indicating obesity or overweight had enrichment in Bifidobacterium bifidum and B. adolescentis. Women with BMI > 25 kg/m2 had a higher abundance of microbiota that support biotin synthesis and regulate epithelial cells in the lower gastrointestinal tract. These epithelial cells are responsible for host adaptability to dietary lipid variation and caloric absorption. CONCLUSIONS Our analysis suggests that there are differences in microbial composition and function between BMI groups. Future research should consider how these changes contribute to specific clinical outcomes during pregnancy.
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Affiliation(s)
- Caitlin Dreisbach
- School of NursingUniversity of VirginiaCharlottesvilleVirginiaUSA
- Data Science InstituteColumbia UniversityNew YorkNew YorkUSA
- School of NursingUniversity of RochesterNew YorkNew YorkUSA
| | - Jeanne Alhusen
- School of NursingUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Stephanie Prescott
- College of NursingUniversity of South FloridaTampaFloridaUSA
- Center for Cancer ResearchNational Cancer InstituteBethesdaMarylandUSA
| | - Donald Dudley
- Department of Obstetrics and GynecologyUniversity of Virginia Health SystemCharlottesvilleVirginiaUSA
| | | | - Anna Maria Siega‐Riz
- School of Public Health and Health SciencesUniversity of MassachusettsAmherstMassachusettsUSA
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Wishart DS, Oler E, Peters H, Guo A, Girod S, Han S, Saha S, Lui V, LeVatte M, Gautam V, Kaddurah-Daouk R, Karu N. MiMeDB: the Human Microbial Metabolome Database. Nucleic Acids Res 2022; 51:D611-D620. [PMID: 36215042 PMCID: PMC9825614 DOI: 10.1093/nar/gkac868] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/10/2022] [Accepted: 09/28/2022] [Indexed: 01/29/2023] Open
Abstract
The Human Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, multi-omic, microbiome resource that connects: (i) microbes to microbial genomes; (ii) microbial genomes to microbial metabolites; (iii) microbial metabolites to the human exposome and (iv) all of these 'omes' to human health. MiMeDB was established to consolidate the growing body of data connecting the human microbiome and the chemicals it produces to both health and disease. MiMeDB contains detailed taxonomic, microbiological and body-site location data on most known human microbes (bacteria and fungi). This microbial data is linked to extensive genomic and proteomic sequence data that is closely coupled to colourful interactive chromosomal maps. The database also houses detailed information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that ultimately lead to the observed microbial metabolites in humans. Additional, extensively referenced data about the known or presumptive health effects, measured biosample concentrations and human protein targets for these compounds is provided. All of this information is housed in richly annotated, highly interactive, visually pleasing database that has been designed to be easy to search, easy to browse and easy to navigate. Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases. We believe that MiMeDB represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.
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Affiliation(s)
- David S Wishart
- To whom correspondence should be addressed. Tel: +1 780 492 8574;
| | - Eponine Oler
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Harrison Peters
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - AnChi Guo
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sagan Girod
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Scott Han
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sukanta Saha
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada,Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada
| | - Vicki W Lui
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Marcia LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Rima Kaddurah-Daouk
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Naama Karu
- Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
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Greenwood MP, Hull KL, Brink-Hull M, Lloyd M, Rhode C. Feed and Host Genetics Drive Microbiome Diversity with Resultant Consequences for Production Traits in Mass-Reared Black Soldier Fly ( Hermetia illucens) Larvae. INSECTS 2021; 12:1082. [PMID: 34940170 PMCID: PMC8706267 DOI: 10.3390/insects12121082] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/25/2023]
Abstract
Mass rearing the black soldier fly, Hermetia illucens, for waste bioremediation and valorisation is gaining traction on a global scale. While the health and productivity of this species are underpinned by associations with microbial taxa, little is known about the factors that govern gut microbiome assembly, function, and contributions towards host phenotypic development in actively feeding larvae. In the present study, a 16S rDNA gene sequencing approach applied to a study system incorporating both feed substrate and genetic variation is used to address this knowledge gap. It is determined that the alpha diversity of larval gut bacterial communities is driven primarily by features of the larval feed substrate, including the diversity of exogenous bacterial populations. Microbiome beta diversity, however, demonstrated patterns of differentiation consistent with an influence of diet, larval genetic background, and a potential interaction between these factors. Moreover, evidence for an association between microbiome structure and the rate of larval fat accumulation was uncovered. Taxonomic enrichment analysis and clustering of putative functional gut profiles further suggested that feed-dependent turnover in microbiome communities is most likely to impact larval characteristics. Taken together, these findings indicate that host-microbiome interactions in this species are complex yet relevant to larval trait emergence.
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Affiliation(s)
- Matthew P. Greenwood
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Kelvin L. Hull
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Marissa Brink-Hull
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
| | - Melissa Lloyd
- Insect Technology Group Holdings UK Ltd., 1 Farnham Road, Guildford, Surrey GU2 4RG, UK;
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (M.P.G.); (K.L.H.); (M.B.-H.)
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Soto-Avila L, Merce RC, Santos W, Castañeda N, Gutierrez-Ríos RM. Distribution and preservation of the components of the engulfment. What is beyond representative genomes? PLoS One 2021; 16:e0246651. [PMID: 33651833 PMCID: PMC7924749 DOI: 10.1371/journal.pone.0246651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2021] [Indexed: 12/16/2022] Open
Abstract
Engulfment requires the coordinated, targeted synthesis and degradation of peptidoglycan at the leading edge of the engulfing membrane to allow the mother cell to completely engulf the forespore. Proteins such as the DMP and Q:AH complexes in Bacillus subtilis are essential for engulfment, as are a set of accessory proteins including GerM and SpoIIB, among others. Experimental and bioinformatic studies of these proteins in bacteria distinct from Bacillus subtilis indicate that fundamental differences exist regarding the organization and mechanisms used to successfully perform engulfment. As a consequence, the distribution and prevalence of the proteins involved in engulfment and other proteins that participate in different sporulation stages have been studied using bioinformatic approaches. These works are based on the prediction of orthologs in the genomes of representative Firmicutes and have been helpful in tracing hypotheses about the origin and evolution of sporulation genes, some of which have been postulated as sporulation signatures. To date, an extensive study of these signatures outside of the representative Firmicutes is not available. Here, we asked whether phyletic profiles of proteins involved in engulfment can be used as signatures able to describe the sporulation phenotype. We tested this hypothesis in a set of 954 Firmicutes, finding preserved phyletic profiles defining signatures at the genus level. Finally, a phylogenetic reconstruction based on non-redundant phyletic profiles at the family level shows the non-monophyletic origin of these proteins due to gain/loss events along the phylum Firmicutes.
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Affiliation(s)
- Lizeth Soto-Avila
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
- Centro de Investigacion en Dinamica Celular, Instituto de Investigacion en Ciencias Basicas y Aplicadas, Universidad Autonoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Ricardo Ciria Merce
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Walter Santos
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Nori Castañeda
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Rosa-María Gutierrez-Ríos
- Departamento de Microbiologia Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
- * E-mail:
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Hartman LM, van Oppen MJH, Blackall LL. Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef. Anim Microbiome 2020; 2:10. [PMID: 33499977 PMCID: PMC7807684 DOI: 10.1186/s42523-020-00029-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/17/2020] [Indexed: 02/04/2023] Open
Abstract
Background Coral reefs have sustained damage of increasing scale and frequency due to climate change, thereby intensifying the need to elucidate corals’ biological characteristics, including their thermal tolerance and microbial symbioses. The sea anemone, Exaiptasia diaphana, has proven an ideal coral model for many studies due to its close phylogenetic relationship and shared traits, such as symbiosis with algae of the family Symbiodiniaceae. However, established E. diaphana clonal lines are not available in Australia thus limiting the ability of Australian scientists to conduct research with this model. To help address this, the bacterial and Symbiodiniaceae associates of four Great Barrier Reef (GBR)-sourced E. diaphana genotypes established in laboratory aquaria and designated AIMS1–4, and from proxies of wild GBR E. diaphana were identified by metabarcoding of the bacterial 16S rRNA gene and eukaryotic rRNA gene ITS2 region. The relationship between AIMS1–4 and their bacterial associates was investigated, as was bacterial community phenotypic potential. Existing data from two existing anemone clonal lines, CC7 and H2, were included for comparison. Results Overall, 2238 bacterial amplicon sequence variants (ASVs) were observed in the AIMS1–4 bacterial communities, which were dominated by Proteobacteria and Bacteroidetes, together comprising > 90% relative abundance. Although many low abundance bacterial taxa varied between the anemone genotypes, the AIMS1–4 communities did not differ significantly. A significant tank effect was identified, indicating an environmental effect on the microbial communities. Bacterial community richness was lower in all lab-maintained E. diaphana compared to the wild proxies, suggesting a reduction in bacterial diversity and community phenotypic potential due to culturing. Seventeen ASVs were common to every GBR lab-cultured anemone, however five were associated with the Artemia feedstock, making their specific association to E. diaphana uncertain. The dominant Symbiodiniaceae symbiont in all GBR anemones was Breviolum minutum. Conclusion Despite differences in the presence and abundance of low abundance taxa, the bacterial communities of GBR-sourced lab-cultured E. diaphana are generally uniform and comparable to communities reported for other lab-cultured E. diaphana. The data presented here add to the global E. diaphana knowledge base and make an important contribution to the establishment of a GBR-sourced coral model organism.
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Affiliation(s)
- Leon Michael Hartman
- Swinburne University of Technology, Melbourne, Australia. .,The University of Melbourne, Melbourne, Australia.
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Skwark MJ, Torres PHM, Copoiu L, Bannerman B, Floto RA, Blundell TL. Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. Database (Oxford) 2019; 2019:5611286. [PMID: 31681953 PMCID: PMC6853642 DOI: 10.1093/database/baz113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/31/2019] [Accepted: 08/28/2019] [Indexed: 02/02/2023]
Abstract
Mycobacterium abscessus, a rapid growing, multidrug resistant, nontuberculous mycobacteria, can cause a wide range of opportunistic infections, particularly in immunocompromised individuals. M. abscessus has emerged as a growing threat to patients with cystic fibrosis, where it causes accelerated inflammatory lung damage, is difficult and sometimes impossible to treat and can prevent safe transplantation. There is therefore an urgent unmet need to develop new therapeutic strategies. The elucidation of the M. abscessus genome in 2009 opened a wide range of research possibilities in the field of drug discovery that can be more effectively exploited upon the characterization of the structural proteome. Where there are no experimental structures, we have used the available amino acid sequences to create 3D models of the majority of the remaining proteins that constitute the M. abscessus proteome (3394 proteins and over 13 000 models) using a range of up-to-date computational tools, many developed by our own group. The models are freely available for download in an on-line database, together with quality data and functional annotation. Furthermore, we have developed an intuitive and user-friendly web interface (http://www.mabellinidb.science) that enables easy browsing, querying and retrieval of the proteins of interest. We believe that this resource will be of use in evaluating the prospective targets for design of antimicrobial agents and will serve as a cornerstone to support the development of new molecules to treat M. abscessus infections.
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Affiliation(s)
- Marcin J Skwark
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Pedro H M Torres
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Liviu Copoiu
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Bridget Bannerman
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - R Andres Floto
- Molecular Immunity Unit, Department of Medicine University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
and,Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK,Corresponding author: Tel: +44 1223 333628; Fax: +44 1223 766002;
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Functional Characterization and Structural Analysis of NADH Oxidase Mutants from Thermus thermophilus HB27: Role of Residues 166, 174, and 194 in the Catalytic Properties and Thermostability. Microorganisms 2019; 7:microorganisms7110515. [PMID: 31683638 PMCID: PMC6921046 DOI: 10.3390/microorganisms7110515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/16/2022] Open
Abstract
The Thermus thermophilus strain HB27 NADH-oxidase (Tt27-NOX) catalyzes the oxidation of nicotinamide adenine dinucleotide (NAD(P)H) by reducing molecular oxygen to hydrogen peroxide in a two-electron transfer mechanism. Surprisingly, Tt27-NOX showed significant differences in catalytic properties compared to its counterpart from the strain HB8 (Tt8-NOX), despite a high degree of sequence homology between both variants. The sequence comparison between both enzymes revealed only three divergent amino acid residues at positions 166, 174, and 194. Motivated with these findings, in this work we performed mutagenesis experiments in the former three positions to study the specific role of these residues in the catalytic properties and thermostability of Tt27-NOX. We subjected five mutants, along with the wild-type enzyme, to biochemical characterization and thermal stability studies. As a result, we identified two more active and more thermostable variants than any Tt8-NOX variant reported in the literature. The most active and thermostable variant K166/H174/Y194 retained 90% of its initial activity after 5 h at pH 7 and 80 °C and an increase in melting temperature of 48.3 °C compared with the least active variant K166/R174/Y194 (inactivated after 15 min of incubation). These results, supported by structural analysis and molecular dynamics simulation studies, suggest that Lys at position 166 may stabilize the loop in which His174 is located, increasing thermal stability.
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Shin J, Jang HM, Shin SG, Kim YM. Thermophilic anaerobic digestion: Effect of start-up strategies on performance and microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:87-95. [PMID: 31203011 DOI: 10.1016/j.scitotenv.2019.05.428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Effects of two different start-up methods were compared during conversion from mesophilic to thermophilic anaerobic digestion of sewage sludge. During the batch operation, a transient increase in both total bacterial concentration and relative abundance of thermophilic bacteria in R1 (a one-step increase method) resulted in 34% higher volatile solids (VS) removal efficiency by R1 compared to R2 (a step-wise increase method). Meanwhile, higher total archaeal concentration and increased relative abundance of thermophilic archaea in R2 were attributed to 65% higher methane production by R2 compared to R1. The same trends for VS removal and methane production were observed during the subsequent continuous mode, although the microbial composition of the two reactors became similar. These findings may prove helpful for determining the preferred start-up method for thermophilic anaerobic digestion: a one-step method can be proposed for higher VS removal efficiency, or a step-wise method can be selected for enhanced methane production.
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Affiliation(s)
- Jingyeong Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea
| | - Hyun Min Jang
- Department of Agricultural and Biological Engineering, Texas A&M AgriLife Research Center at Stephenville, Texas A&M University, USA
| | - Seung Gu Shin
- Department of Energy Engineering, Gyeongnam National University of Science and Technology, Jinju, Gyeongnam, Republic of Korea.
| | - Young Mo Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 500-712, Republic of Korea.
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Brink M, Rhode C, Macey BM, Christison KW, Roodt-Wilding R. Metagenomic assessment of body surface bacterial communities of the sea urchin, Tripneustes gratilla. Mar Genomics 2019; 47:100675. [PMID: 30962029 DOI: 10.1016/j.margen.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022]
Abstract
Sea urchins, including Tripneustes gratilla, are susceptible to a disease known as bald sea urchin disease, which has the potential to lead to economic losses in this emerging aquaculture industry in South Africa. This disease is characterized by lesions that form on sea urchin exoskeletal surfaces. This study aimed to characterize the body surface bacterial communities associated with T. gratilla, using a 16S rDNA gene metagenomics approach, to provide insight into the bacterial agents associated with this aquaculture species, as well as with this balding disease. Bacterial samples were collected from non-lesioned healthy animals obtained from natural locations along the eastern coast of South Africa, as well as from different cultured cohorts: non-lesioned healthy-, lesioned diseased- and non-lesioned stressed animals. A total of 1,067,515 individual bacterial operational taxonomic units (OTUs) were identified, belonging to 133 family-, 123 genus- and 113 species level OTU groups. Alpha diversity analyses, based on Chao1, Shannon and Simpson indices, showed that there were no statistically significant differences (ANOVA; P > 0.05) between the respective cohorts, as all cohorts displayed a high degree of bacterial diversity. Similarly, beta diversity analyses (Non-metric multidimensional scaling) showed a large degree of overlapping OTUs across the four cohorts. Within each cohort, various OTUs commonly associated with marine environments were found, predominantly belonging to the families Vibrionaceae, Saprospiraceae, Flavobacteriaceae and Sphingomonadaceae. Differential abundance analysis (DESeq2) revealed that OTUs that are differentially abundant across cohorts were likely not responsible for this balding disease, suggesting that complex bacterial agents, rather than a specific pathogenic agent, are likely causing this disease. Furthermore, the putative metabolic functions assigned to the bacterial communities showed that heterotrophic bacteria appear to be responsible for tissue lysis of degrading animal matter. The results from this study, obtained through univariate and multivariate-based approaches, contributes to future management strategies of this emerging aquaculture species by providing insight into the bacterial communities associated with both natural and cultured environments.
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Affiliation(s)
- M Brink
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - C Rhode
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa
| | - B M Macey
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa
| | - K W Christison
- Department of Agriculture, Forestry and Fisheries, Aquaculture Research, Private Bag X2, Roggebaai, Western Cape 8012, South Africa; Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - R Roodt-Wilding
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Private Bag X1, Stellenbosch, Western Cape 7602, South Africa.
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11
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Supek F. The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function. J Mol Evol 2015; 82:65-73. [PMID: 26538122 DOI: 10.1007/s00239-015-9714-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023]
Abstract
Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell.
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Affiliation(s)
- Fran Supek
- Division of electronics, Rudjer Boskovic Institute, 10000, Zagreb, Croatia.
- EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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12
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Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes. BMC Genomics 2015; 16:773. [PMID: 26459834 PMCID: PMC4603813 DOI: 10.1186/s12864-015-1957-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 09/28/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Bacterial infections comprise a global health challenge as the incidences of antibiotic resistance increase. Pathogenic potential of bacteria has been shown to be context dependent, varying in response to environment and even within the strains of the same genus. RESULTS We used the KEGG repository and extensive literature searches to identify among the 2527 bacterial genomes in the literature those implicated as pathogenic to the host, including those which show pathogenicity in a context dependent manner. Using data on the gene contents of these genomes, we identified sets of genes highly abundant in pathogenic but relatively absent in commensal strains and vice versa. In addition, we carried out genome comparison within a genus for the seventeen largest genera in our genome collection. We projected the resultant lists of ortholog genes onto KEGG bacterial pathways to identify clusters and circuits, which can be linked to either pathogenicity or synergy. Gene circuits relatively abundant in nonpathogenic bacteria often mediated biosynthesis of antibiotics. Other synergy-linked circuits reduced drug-induced toxicity. Pathogen-abundant gene circuits included modules in one-carbon folate, two-component system, type-3 secretion system, and peptidoglycan biosynthesis. Antibiotics-resistant bacterial strains possessed genes modulating phagocytosis, vesicle trafficking, cytoskeletal reorganization, and regulation of the inflammatory response. Our study also identified bacterial genera containing a circuit, elements of which were previously linked to Alzheimer's disease. CONCLUSIONS Present study produces for the first time, a signature, in the form of a robust list of gene circuitry whose presence or absence could potentially define the pathogenicity of a microbiome. Extensive literature search substantiated a bulk majority of the commensal and pathogenic circuitry in our predicted list. Scanning microbiome libraries for these circuitry motifs will provide further insights into the complex and context dependent pathogenicity of bacteria.
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Nakamura H, Balskus EP. Using Chemical Knowledge to Uncover New Biological Function: Discovery of the Cylindrocyclophane Biosynthetic Pathway. Synlett 2013; 24:1464-1470. [PMID: 31723311 PMCID: PMC6853628 DOI: 10.1055/s-0033-1338879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
An understanding of organic chemistry can play a central role in uncovering enzymes with new biochemical functions. We have recently identified the enzymes involved in the biosynthesis of the cylindrocyclophanes, a structurally unique family of natural products, and found that this pathway employs a remarkable macrocyclization event that requires functionalization of an unactivated carbon atom. This work illustrates the potential of using chemically guided approaches for enzyme discovery.
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Affiliation(s)
- Hitomi Nakamura
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Emily P Balskus
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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Busby B, Kristensen DM, Koonin EV. Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. Environ Microbiol 2012; 15:307-12. [PMID: 23035931 DOI: 10.1111/j.1462-2920.2012.02886.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Facultative pathogens have extremely dynamic pan-genomes, to a large extent derived from bacteriophages and other mobile elements. We developed a simple approach to identify phage-derived genomic islands and apply it to show that pathogens from diverse bacterial genera are significantly enriched in clustered phage-derived genes compared with related benign strains. These findings show that genome expansion by integration of prophages containing virulence factors is a major route of evolution of facultative bacterial pathogens.
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Affiliation(s)
- Ben Busby
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Arndt D, Xia J, Liu Y, Zhou Y, Guo AC, Cruz JA, Sinelnikov I, Budwill K, Nesbø CL, Wishart DS. METAGENassist: a comprehensive web server for comparative metagenomics. Nucleic Acids Res 2012; 40:W88-95. [PMID: 22645318 PMCID: PMC3394294 DOI: 10.1093/nar/gks497] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca.
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Affiliation(s)
- David Arndt
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
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